Sensitivity of RT-PCR tests for SARS-CoV-2 through time.

Reverse transcriptase polymerase chain reaction (RT-PCR) tests are the gold standard for detecting recent infection with SARS-CoV-2. RT-PCR sensitivity varies over the course of an individual's infection, related to changes in viral load. Differences in testing methods, and individual-level variables such as age, may also affect sensitivity. Using data from New Zealand, we estimate the time-varying sensitivity of SARS-CoV-2 RT-PCR under varying temporal, biological and demographic factors. Sensitivity peaks 4-5 days post-infection at 92.7% [91.4%, 94.0%] and remains over 88% between 5 and 14 days post-infection. After the peak, sensitivity declined more rapidly in vaccinated cases compared to unvaccinated, females compared to males, those aged under 40 compared to over 40 s, and Pacific peoples compared to other ethnicities. RT-PCR remains a sensitive technique and has been an effective tool in New Zealand's border and post-border measures to control COVID-19. Our results inform model parameters and decisions concerning routine testing frequency.

The utility of 1-minute sit-to-stand test to detect exerciseinduced oxygen desaturation in outpatient assessment of post COVID-19 patients

Introduction: The 6-min walk test (6MWT) is the gold standard for assessing exercise-induced impairment of gas exchange, but it is technically challenging in a busy outpatient clinic. The aim of this study was to compare the 1-min sit-to-stand test (1STST) with the 6MWT in assessment of exercise-induced oxygen desaturation in post COVID-19 patients in an outpatient setting. Method(s): A total of 447 outpatient post COVID-19 patients were recruited from post COVID-19 clinic. Both 6MWT and 1STST (a set) were performed on the same day including pulse oxygen saturation (SpO2) recording at baseline, nadir, and recovery stage. Result(s): A total of 447 sets were performed at a mean of 160 days post discharge. Majority were in category severe (n=251, 56%), critical (n=118, 26%) and moderate (n=6, 15%). At assessment, most patients were symptomatic (mMRC > 2) n= 258, 58%. There was no significant difference between nadir SpO2 for 6MWT and 1STST (p<0.075) with Bland-Altman plots showing good agreement, p<0.593 (figure 1). There was good correlation between SpO2 and 6MWT or 1STST at baseline;R=0.592 p<0.001, nadir;R=0.456 p<0.001, and recovery;R= 0.514 p<001. 1STST had 76.8% sensitivity and 42.4% specificity to detect > 4% oxygen desaturation compared with 6MWT (table 1). There was also correlation between 6MWT distance and 1STST repetition;R=0.144 p<0.002. Conclusion(s): Both 6MWT and 1STS have good agreement on nadir SpO2 and are sensitive to detect > 4% oxygen desaturation. Therefore, 1STST is an useful screening test to detect exercise-induced oxygen desaturation during outpatient assessment.

The relationship between the ratio of neutrophil to lymphocyte and platelet to acute kidney injury associated with sepsis

Introduction: Sepsis refers to systemic inflammatory reactions caused by infections, which was the common complication after severe infections, trauma, burns, shock, and major surgery. Septic shock and multiple organ dysfunction syndromes associated with sepsis and its progression were common in intensive care units (ICU). Acute kidney injury (AKI) was a common complication of sepsis. The clinical mortality rate for sepsis was about 20%-50%, and may be as high as 70% if sepsis was associated with acute kidney injury (S-AKI). Therefore, there was a need to initiate the diagnosis and risk stratification of AKI in patients with sepsis, which will contribute to effective intervention and good prognosis. Currently, although the treatment of S-AKI was becoming better understood, diagnostic criteria for AKI were still based on elevated serum creatinine levels or decreased urine volume with the low sensitivity and specificity. Therefore, the use of current diagnostic criteria was not sufficient. The ratio of neutrophils to lymphocytes and platelets (N/LP) was a low-cost measure that could be obtained through routine blood tests and is often used to reflect the inflammatory state of the body. Its usefulness as a predictor of COVID-19 prognosis and the incidence of AKI after abdominal and cardiovascular surgery has been demonstrated. The aim of this study was to determine whether elevated N/LP is associated with the risk and severity of S-AKI within 7 days after admission to the ICU of adult sepsis patients in the Department of Intensive Care Medicine, the First Affiliated Hospital of Soochow University. Method(s): Statistical analysis was performed using SPSS22.0. Data with a normal distribution were expressed as mean +/- standard deviation, and data without a normal distribution was expressed as median and interquartile distance (IQR). When variables has normal distributions and homogenous variances, the independent sample T-test and one-way ANOVA were used to compare the means, and then the minimum significant difference (LSD) test was performed. The rank sum test was used to compare variables with non-normal distribution. P value below 0.05(*) was considered statistically significant. Result(s): A total of 45 patients with sepsis from 2021/01/1-2021/12/31 were enrolled in the first ward of Intensive Care Department of the First Affiliated Hospital of Soochow University, among which 20 patients with sepsis developed AKI within 7 days after admission to ICU. The N/LP values of sepsis patients and S-AKI patients did not conform to the normal distribution, but satisfied the normal distribution after logarithmic conversion. Independent sample T test showed that there was a significant difference between the two groups. Further comparison was made between patients with sepsis and patients with S-AKI at each stage. The data were in line with normal distribution after logarithmic conversion, and statistical difference was found after one-way ANOVA. There were significant increases in S-AKI3 stage compared with sepsis patients, S-AKI3 stage compared with S-AKI2 stage and S-AKI3 stage compared with S-AKI1 stage. Conclusion(s): Elevated N/LP levels may be associated with the development of S-AKI and severe AKI in patients with sepsis within 7 days after admission to ICU. No conflict of interestCopyright © 2023

Diagnostic accuracy of vaccine and vaccine excipient testing in the setting of allergic reactions to COVID-19 vaccines: A systematic review and meta-analysis.

For persons with immediate allergic reactions to mRNA COVID-19 vaccines, skin testing (ST) to the vaccine/excipients (polyethylene glycol[PEG] and polysorbate 80 [PS]) has been recommended, but has unknown accuracy. To assess vaccine/excipient ST accuracy in predicting all-severity immediate allergic reactions upon re-vaccination, systematic review was performed searching Medline, EMBASE, Web of Science, and the WHO global coronavirus database (inception-Oct 4, 2021) for studies addressing immediate (≤4 h post-vaccination) all-severity allergic reactions to 2nd mRNA COVID-19 vaccination in persons with 1st dose immediate allergic reactions. Cases evaluating delayed reactions, change of vaccine platform, or revaccination without vaccine/excipient ST were excluded. Meta-analysis of diagnostic testing accuracy was performed using Bayesian methods. The GRADE approach evaluated certainty of the evidence, and QUADAS-2 assessed risk of bias. Among 20 studies of mRNA COVID-19 first dose vaccine reactions, 317 individuals underwent 578 ST to any one or combination of vaccine, PEG, or PS, and were re-vaccinated with the same vaccine. Test sensitivity for either mRNA vaccine was 0.2 (95%CrI 0.01-0.52) and specificity 0.97 (95%CrI 0.9-1). PEG test sensitivity was 0.02 (95%CrI 0.00-0.07) and specificity 0.99 (95%CrI 0.96-1). PS test sensitivity was 0.03 (95%CrI 0.00-0.0.11) and specificity 0.97 (95%CrI 0.91-1). Combined for use of any of the 3 testing agents, sensitivity was 0.03 (95%CrI 0.00-0.08) and specificity was 0.98 (95%CrI 0.95-1.00). Certainty of evidence was moderate. ST has low sensitivity but high specificity in predicting all-severity repeat immediate allergic reactions to the same agent, among persons with 1st dose immediate allergic reactions to mRNA COVID-19 vaccines. mRNA COVID-19 vaccine or excipient ST has limited risk assessment utility.

Optimal group testing strategy for the mass screening of SARS-CoV-2.

We analyze the group testing strategy that maximizes the efficiency of the SARS-CoV-2 screening test while ensuring its effectiveness, where the effectiveness of group testing guarantees that negative results from pooled samples can be considered presumptive negative. Two aspects of test efficiency are considered, one concerning the maximization of the welfare throughput and the other concerning the maximization of the identification rate (namely, identifying as many infected individuals as possible). We show that compared with individual testing, group testing leads to a higher probability of false negative results but a lower probability of false positive results. To ensure the test effectiveness, both the group size and the prevalence of SARS-CoV-2 must be below certain respective thresholds. To achieve test efficiency that concerns either the welfare throughput maximization or the identification rate maximization, the optimal group size is jointly determined by the test accuracy parameters, the infection prevalence rate, and the relative importance of identifying infected subjects. We also show that the optimal group size that maximizes the welfare throughput is weakly smaller than the one that maximizes the identification rate.

On the Test Accuracy and Effective Control of the COVID-19 Pandemic: A Case Study in Singapore

This study examines the impact of coronavirus disease 2019 (COVTD-19) test accuracy (i.e., sensitivity and specificity) on the progression of the pandemic under two scenarios of limited and unlimited test capacity. We extend the classic susceptible-exposed-infectious-recovered model to incorporate test accuracy and compare the progression of the pandemic under various sensitivities and specificities. We find that high-sensitivity tests effectively reduce the total number of infections only with sufficient testing capacity. Nevertheless, with limited test capacity and a relatively high cross-infection rate, the total number of infected cases may increase when sensitivity is above a certain threshold. Despite the potential for higher sensitivity tests to identify more infected individuals, more false positive cases occur, which wastes limited testing capacity, slowing down the detection of infected cases. Our findings reveal that improving test sensitivity alone does not always lead to effective pandemic control, indicating that policymakers should balance the trade-off between high sensitivity and high false positive rates when designing containment measures for infectious diseases, such as COVID-19, particularly when navigating limited test capacity.

Rapid comparative evaluation of SARS-CoV-2 rapid point-of-care antigen tests.

PURPOSE: The objective of this study was to develop a scalable approach for direct comparison of the analytical sensitivities of commercially available SARS-CoV-2 antigen point-of-care tests (AgPOCTs) to rapidly identify poor-performing products. METHODS: We present a methodology for quick assessment of the sensitivity of SARS-CoV-2 AgPOCTs suitable for quality evaluation of many different products. We established reference samples with high, medium, and low SARS-CoV-2 viral loads along with a SARS-CoV-2 negative control sample. Test samples were used to semi-quantitatively assess the analytical sensitivities of 32 different commercial AgPOCTs in a head-to-head comparison. RESULTS: Among 32 SARS-CoV-2 AgPOCTs tested, we observe sensitivity differences across a broad range of viral loads (9.8 × 108 to 1.8 × 105 SARS-CoV-2 genome copies per ml). 23 AgPOCTs detected the Ct25 test sample (1.6 × 106 copies/ml), while only five tests detected the Ct28 test sample (1.8 × 105 copies/ml). In the low-range of analytical sensitivity, we found three saliva spit tests only delivering positive results for the Ct21 sample (2.7 × 107 copies/ml). Comparison with published data supports our AgPOCT ranking. Importantly, we identified an AgPOCT widely offered, which did not reliably recognize the sample with the highest viral load (Ct16 test sample with 9.8 × 108 copies/ml) leading to serious doubts about its usefulness in SARS-CoV-2 diagnostics. CONCLUSION: The results show that the rapid sensitivity assessment procedure presented here provides useful estimations on the analytical sensitivities of 32 AgPOCTs and identified a widely-spread AgPOCT with concerningly low sensitivity.

Factors that Influence the Reported Sensitivity of Rapid Antigen Testing for SARS-CoV-2.

Tests that detect the presence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) antigen in clinical specimens from the upper respiratory tract can provide a rapid means of coronavirus disease 2019 (COVID-19) diagnosis and help identify individuals who may be infectious and should isolate to prevent SARS-CoV-2 transmission. This systematic review assesses the diagnostic accuracy of SARS-CoV-2 antigen detection in COVID-19 symptomatic and asymptomatic individuals compared to quantitative reverse transcription polymerase chain reaction (RT-qPCR) and summarizes antigen test sensitivity using meta-regression. In total, 83 studies were included that compared SARS-CoV-2 rapid antigen-based lateral flow testing (RALFT) to RT-qPCR for SARS-CoV-2. Generally, the quality of the evaluated studies was inconsistent; nevertheless, the overall sensitivity for RALFT was determined to be 75.0% (95% confidence interval: 71.0-78.0). Additionally, RALFT sensitivity was found to be higher for symptomatic vs. asymptomatic individuals and was higher for a symptomatic population within 7 days from symptom onset compared to a population with extended days of symptoms. Viral load was found to be the most important factor for determining SARS-CoV-2 antigen test sensitivity. Other design factors, such as specimen storage and anatomical collection type, also affect the performance of RALFT. RALFT and RT-qPCR testing both achieve high sensitivity when compared to SARS-CoV-2 viral culture.

Diurnal Variation in SARS-CoV-2 PCR Test Results: Test Accuracy May Vary by Time of Day.

False negative tests for SARS-CoV-2 are common and have important public health and medical implications. We tested the hypothesis of diurnal variation in viral shedding by assessing the proportion of positive versus negative SARS-CoV-2 reverse transcription polymerase chain reaction (RT-PCR) tests and cycle time (Ct) values among positive samples by the time of day. Among 86,342 clinical tests performed among symptomatic and asymptomatic patients in a regional health care network in the southeastern United States from March to August 2020, we found evidence for diurnal variation in the proportion of positive SARS-CoV-2 tests, with a peak around 1400 h and 1.7-fold variation over the day after adjustment for age, sex, race, testing location, month, and day of week and lower Ct values during the day for positive samples. These findings have important implications for public health testing and vaccination strategies.

Longitudinal Assessment of Diagnostic Test Performance Over the Course of Acute SARS-CoV-2 Infection.

BACKGROUND: Serial screening is critical for restricting spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by facilitating timely identification of infected individuals to interrupt transmission. Variation in sensitivity of different diagnostic tests at different stages of infection has not been well documented. METHODS: In a longitudinal study of 43 adults newly infected with SARS-CoV-2, all provided daily saliva and nasal swabs for quantitative reverse transcription polymerase chain reaction (RT-qPCR), Quidel SARS Sofia antigen fluorescent immunoassay (FIA), and live virus culture. RESULTS: Both RT-qPCR and Quidel SARS Sofia antigen FIA peaked in sensitivity during the period in which live virus was detected in nasal swabs, but sensitivity of RT-qPCR tests rose more rapidly prior to this period. We also found that serial testing multiple times per week increases the sensitivity of antigen tests. CONCLUSIONS: RT-qPCR tests are more effective than antigen tests at identifying infected individuals prior to or early during the infectious period and thus for minimizing forward transmission (given timely results reporting). All tests showed >98% sensitivity for identifying infected individuals if used at least every 3 days. Daily screening using antigen tests can achieve approximately 90% sensitivity for identifying infected individuals while they are viral culture positive.

Quantifying the Impact of Nasopharyngeal Specimen Quality on Severe Acute Respiratory Syndrome Coronavirus 2 Test Performance.

BACKGROUND: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reverse-transcription polymerase chain reaction (RT-PCR) cycle threshold (Ct) has been used to estimate quantitative viral load, with the goal of targeting isolation precautions for individuals with coronavirus disease 2019 (COVID-19) and guiding public health interventions. However, variability in specimen quality can alter the Ct values obtained from SARS-CoV-2 clinical assays. We sought to define how variable nasopharyngeal (NP) swab quality impacts clinical SARS-CoV-2 test sensitivity. METHODS: We performed amplification of a human gene target (ß-actin) in parallel with a clinical RT-PCR targeting the SARS-CoV-2 ORF1ab gene for 1282 NP specimens collected from patients with clinical concern for COVID-19. We evaluated the relationship between NP specimen quality, characterized by late Ct values for the human gene target ß-actin Ct, and the probability of SARS-CoV-2 detection via logistic regression, as well as the linear relationship between SARS-CoV-2 and ß-actin Ct. RESULTS: Low-quality NP swabs are less likely to detect SARS-CoV-2 (odds ratio, 0.607 [95% credible interval {CrI}, .487-.753]). We observed a positive linear relationship between SARS-CoV-2 and ß-actin Ct values (slope, 0.181 [95% CrI, .097-.264]), consistent with a reduction in detection of 0.181 cycles for each additional cycle of the ß-actin target. COVID-19 disease severity was not associated with ß-actin Ct values. CONCLUSIONS: Variability in NP specimen quality significantly impacts the performance of clinical SARS-CoV-2 assays, and caution should be taken when interpreting quantitative SARS-CoV-2 Ct results. If unrecognized, low-quality NP specimens, which are characterized by a low level of amplifiable human DNA target, may limit the successful application of SARS-CoV-2 Ct values to direct infection control and public health interventions.

Estimating the effectiveness of routine asymptomatic PCR testing at different frequencies for the detection of SARS-CoV-2 infections.

BACKGROUND: Routine asymptomatic testing using RT-PCR of people who interact with vulnerable populations, such as medical staff in hospitals or care workers in care homes, has been employed to help prevent outbreaks among vulnerable populations. Although the peak sensitivity of RT-PCR can be high, the probability of detecting an infection will vary throughout the course of an infection. The effectiveness of routine asymptomatic testing will therefore depend on testing frequency and how PCR detection varies over time. METHODS: We fitted a Bayesian statistical model to a dataset of twice weekly PCR tests of UK healthcare workers performed by self-administered nasopharyngeal swab, regardless of symptoms. We jointly estimated times of infection and the probability of a positive PCR test over time following infection; we then compared asymptomatic testing strategies by calculating the probability that a symptomatic infection is detected before symptom onset and the probability that an asymptomatic infection is detected within 7 days of infection. RESULTS: We estimated that the probability that the PCR test detected infection peaked at 77% (54-88%) 4 days after infection, decreasing to 50% (38-65%) by 10 days after infection. Our results suggest a substantially higher probability of detecting infections 1-3 days after infection than previously published estimates. We estimated that testing every other day would detect 57% (33-76%) of symptomatic cases prior to onset and 94% (75-99%) of asymptomatic cases within 7 days if test results were returned within a day. CONCLUSIONS: Our results suggest that routine asymptomatic testing can enable detection of a high proportion of infected individuals early in their infection, provided that the testing is frequent and the time from testing to notification of results is sufficiently fast.

False-negative testing for severe acute respiratory syndrome coronavirus 2: consideration in obstetrical care.

Because the obstetrical population seems to have a high proportion of asymptomatic patients who are carriers of severe acute respiratory syndrome coronavirus 2, universal testing has been proposed as a strategy to risk-stratify all obstetrical admissions and guide infection prevention protocols. Here, we describe a case of a critically ill obstetrical patient with all the clinical symptoms of coronavirus disease 2019 and 3 false-negative results of nasopharyngeal swabs for molecular testing. We review and discuss the uncertain clinical characteristics of current severe acute respiratory syndrome coronavirus 2 molecular testing and the implications of false-negative results in the obstetrical population.