Clinical performance and potential of a SARS-CoV-2 detection kit without RNA purification steps

Objectives Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is rapidly spreading globally. Early diagnosis plays an essential role in controlling the infection. Therefore, early and accurate SARS-CoV-2 detection assays along with easy operation are required. The aim of this study was to compare the clinical performance of the Ampdirect™ 2019-nCoV Detection Kit (SHIMADZU assay), which does not require RNA purification steps, with that of the preexisting SARS-CoV-2 detection assays, which use a purified RNA template. Methods A total of 71 samples (65 nasopharyngeal specimens and 6 sputum specimens) were collected from 32 individuals, including patients infected with SARS-CoV-2 and those with suspected infection. The sensitivity and kappa (κ) coefficient were assessed between the SARS-CoV-2 detection assays using the reference standard, which was defined as a true positive result by any one of the four SARS-CoV-2 detection assays. Results The overall sensitivity and κ coefficient of the SHIMADZU assay were 86.0% (95% confidence interval [CI]: 77.9–94.2) and 0.83 (95% CI: 0.69–0.96), respectively. In particular, among the 18 samples collected within 10 days from symptom onset, the sensitivity and κ coefficient of the SHIMADZU assay were 100% and 1.0, respectively. Conclusions Although a relatively small number of samples was evaluated, the SHIMADZU assay showed good analytical performance and as such would be highly useful for the detection of SARS-CoV-2. The test can be performed easily and quickly and has the potential for future applications in situations where a highly sensitive diagnosis is required.

Referral Criteria for Preschool Hearing Screening in Resource-Constrained Settings: A Comparison of Protocols

Purpose This study aimed to describe and compare the performance of two screening protocols used for preschool hearing screening in resource-constrained settings. Method Secondary data analysis was done to determine the performance of two protocols implemented during a preschool hearing screening program using mobile health technology in South Africa. Pure-tone audiometry screening at 25 dB HL for 1000, 2000, and 4000 Hz in each ear was used by both protocols. The fail criterion for the first protocol (2,147 children screened) constituted a no-response on one or more frequencies in either ear. The second protocol required two or more no-responses (5,782 children). Multivariate logistic regression models were used to investigate associations between outcomes and protocol, age, gender, and duration. Results Fail rates for the one-frequency fail protocol was 8.7% ( n = 186) and 4.3% ( n = 250) for the two-frequency fail protocol. Children screened with the two-frequency fail protocol were 52.9% less likely to fail ( p < .001; OR = 0.471; 95% confidence interval [0.385, 0.575]). Gender ( p = .251) and age ( p = .570) had no significant effect on screening outcome. A percentage of cases screened (44.7%) exceeded permissible noise levels in at least one ear at 1000 Hz across both protocols. True- and false-positive cases did not differ significantly between protocols. Protocol type ( p = .204), gender ( p = .314), and age ( p = .982) did not affect the odds of being a true-positive result. Average screening time was 72.8 s (78.66 SD ) and 64.9 s (55.78 SD ) for the one-frequency and two-frequency fail protocols, respectively. Conclusions A two-frequency fail criterion and immediate rescreen of failed frequencies significantly reduced referral rate for follow-up services that are often overburdened in resourced-constrained settings. Future protocol adaptations can also consider increasing the screening levels at 1000 Hz to minimize the influence of environmental noise.

Early Warning of Suspected Doping from Biological Passport Based on Multivariate Trends

The indirect identification of doping in sports can be performed by assessing athletesʼ hematological perturbations from the analysis of blood collected on different occasions. Because prosecution for doping based on this information requires expensive and time-consuming interpretation of blood analysis results by various expert hematologists, mathematical data screening is performed to decide which cases should be forwarded to hematologists. The current Bayesian and univariate screening of data does not process the multivariate trends of blood parameters or take the time interval between samplings into account. This work presents a computational tool that overcomes these limitations by calculating a single score, the hematological perturbation index (HPIx), for which a threshold is defined above which hematologists should be asked to assess the athleteʼs biological passport. The doping detection from this index, normalized for days difference between samplings based on 3, 4 or 5 consecutive samplings, is associated with true positive result rates (TP) not below 98% and false positive result rates (FP) less than 0.9%. Therefore, this tool can be useful as an early warning system of hematological perturbations to decide which athletes should be more closely monitored and which biological passports should be forwarded to hematologists for medical interpretation of data.

236. The Comparative Utility Of Metagenomic Next-Generation Sequencing and Universal PCR for Pathogen Detection on Cerebrospinal Fluid: A Retrospective Analysis From a Tertiary Care Center

Background Many neurologic syndromes are underpinned by infectious etiologies that are difficult to diagnose. Broad-range, universal PCR (uPCR), and metagenomic next-generation sequencing (mNGS) are emerging molecular techniques that may allow for enhanced pathogen detection in challenging cases. To date, their comparative clinical utility for pathogen detection in cerebrospinal fluid (CSF) has not been described. Methods We searched the electronic medical record at University of California, San Francisco for all patients who had mNGS and uPCR results available from the same CSF specimen. Using all available clinical information, patients’ clinical episodes were categorized into one of four categories: (1) confirmed central nervous system (CNS) infection, (2) likely CNS infection, (3) confirmed/likely noninfectious etiology, (4) unknown etiology. We also determined whether mNGS and/or uPCR results changed clinical management. Results We identified 75 patients with 78 paired mNGS and uPCR results on CSF. 14/78 (17.9%) had a confirmed CNS infection underpinning their clinical presentation, 11 (14.1%) had a likely CNS infection, 33 (42.3%) had a likely noninfectious cause, and 20 (25.6%) had etiologies that could not be determined. Of the 14 patients with confirmed CNS infection, n = 4 (28.6%) were diagnosed by mNGS and n = 1 (7.1%) by uPCR (Table 1). Most diagnoses missed by mNGS and uPCR were made by CSF serology or from sites other than CSF. Overall, mNGS detected a pathogen in n = 10/78 (12.8%) cases, compared with n = 4/78 (5.1%) using uPCR (Table 2). Among those with a positive mNGS result, n = 6/10 represented a true or likely true positive result, while the remaining were likely contaminants. Of those with a positive uPCR result, n = 1/4 represented a true positive result, while n = 3/4 were likely contaminants. Clinical management was changed by the mNGS or uPCR result in two cases (Table 2). Conclusion mNGS appears to have superior clinical utility to that of universal PCR for pathogen detection in CSF samples, in large part because of additional ability to detect DNA and RNA viruses. Further studies are required to determine the clinical contexts in which mNGS is likely to have maximal diagnostic yield and to better define the utility of uPCR for CNS infections. Disclosures All authors: No reported disclosures.