A systematic review and meta-analysis of the sensitivity of antibody tests for the laboratory confirmation of COVID-19

Aim: The aim of this study was to investigate the utility of serological tests for the diagnosis of COVID-19 during the first week of symptom onset in patients confirmed with the real-time RT-PCR. Materials & methods: A systematic review and meta-analysis of 58 publications were performed using data obtained from Academic Search Ultimate, Africa-wide, Scopus, Web of Science and MEDLINE. Results: We found that the highest pooled sensitivities were obtained with ELISA IgM-IgG and chemiluminescence immunoassay IgM tests. Conclusion: Serological tests have low sensitivity within the first week of symptom onset and cannot replace nucleic acid amplification tests. However, serological assays can be used to support nucleic acid amplification tests.

CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern

We described CRISPR-Cas12-based multiplex allele-specific assay for rapid SARS-CoV-2 variant genotyping. The new system has the potential to be quickly developed, continuously updated, and easily implemented for screening of SARS-CoV-2 variants in resource-limited settings. This approach can be adapted for emerging mutations and implemented in laboratories already conducting SARS-CoV-2 nucleic acid amplification tests using existing resources and extracted nucleic acid.

Multicenter comparison of nucleic acid amplification tests for the diagnosis of rectal and oropharyngeal Chlamydia trachomatis and Neisseria gonorrhoeae infection.

Research using nucleic acid amplification tests (NAATs) have repeatedly found rectal and oropharyngeal infections with Chlamydia trachomatis and Neisseria gonorrhoeae to be common and potentially more difficult to treat than genital infections. Unfortunately, public health and patient care efforts have been hampered by the lack of FDA-cleared NAATs with claims for anorectal or oropharyngeal samples. At the time of the initiation of this study, no commercially available assays had these claims. We formed a novel partnership among academic institutions and diagnostic manufacturers to address this public health need. From May 2018 through August 2019 we recruited 1108 women, 1256 men and 26 transgender persons each of whom provided 3 anal and 3 oropharyngeal swab specimens. The 3 anal swabs were pooled into a single transport tube as were the 3 oropharyngeal swabs. The performance of each of three study assays was estimated by comparison to the composite result and relative to one another. Percent positivity for chlamydia was 5.9 and 1.2% from anal and oropharyngeal specimens, respectively compared to 4.2 and 4.1% for gonorrhea. Sensitivity for chlamydia detection ranged from 81.0-95.1% and 82.8-100% for anal and oropharyngeal specimens, respectively. Gonorrhea sensitivity ranged from 85.9-99.0% and 74.0-100% for anal and oropharyngeal samples, respectively. Specificity estimates were ≥ 98.9% for all assays, organisms and sample types. Although there was heterogeneity between sensitivity estimates, these assays offer better ability to detect extra genital infections than culture and potential solutions for providing appropriate sexual healthcare for populations in which these infections are of concern.

Utility of Point-of-Care COVID-19 Testing in an Outpatient Otolaryngology clinic

Objective To evaluate the utility of point-of-care COVID-19 testing for identifying infected patients in an otolaryngology practice. Study Design Retrospective review of 947 patients tested with a point-of-care nucleic acid amplification test for SARS-CoV-2 (Abbott ID Now). Setting Tertiary otolaryngology clinic setting from July to November 2020. Methods Tests were characterized by provider-specified indication (symptomatic, preprocedural, and universal), subspecialty, provider type, and contemporaneous regional COVID-19 positivity rate, defined as 12%. Positive results were further classified as true or false positive (TP or FP) based on repeat polymerase chain reaction testing wherever available, and true positivity rates were compared among groups by multiway chi-square and Fisher’s exact tests. FP rates within 48 hours of a TP result were also evaluated to assess for batch contamination. Results A total of 947 SARS-CoV-2 nucleic acid amplification tests were performed, yielding 9 TPs (0.95%) and 5 FPs (0.53%). TP rates were significantly different by testing indication, with higher rates among symptomatic patients ( P = .012; vs universal, odds ratio = 7.86 [95% CI, 1.27-83.52]; vs preprocedural, odds ratio = 4.91 [95% CI, 0.79-52.17]); by subspecialty ( P = .011), as driven by higher positivity rates in laryngology; and by encounter, with higher rates among advanced practice practitioners than physicians ( P = .002; odds ratio = 9.97 [95% CI, 2.11-51.16]). TP rates were not significantly different during periods of uncontrolled local outbreak ( P = .660). FP rates were not significantly higher within a 48-hour window of a TP ( P = .192). Conclusion Point-of-care COVID-19 nucleic acid amplification tests in an outpatient otolaryngology clinic identified a low TP rate (<1%) with most cases being clinically suspected. Laryngology and advanced practice practitioner encounters may have higher positivity rates. Level of evidence: 3.

Role of molecular diagnostics in the clinical management of SARS-CoV-2 infection: advantages and drawbacks

The diagnosis of SARS-CoV-2 is based on the use of nucleic acid amplification tests (NAAT), especially rRT-PCR. The latter also allows us to quickly identify variants of concern. However, its use in follow-up of patients and the correlation between Ct value and the viability of the virus is controversial.

The Alpha Variant (B.1.1.7) of SARS-CoV-2 in Children: First Experience from 3544 Nucleic Acid Amplification Tests in a Cohort of Children in Germany

In May 2021, the Alpha variant (B.1.1.7) of SARS-CoV-2 was found in 91% of the SARS-CoV-2 cases in Germany. Not much is known about the symptoms, courses of disease, and infectiousness in pediatric patients with the Alpha variant. Objective: The aim of this retrospective analysis was to gain information on the infection with the Alpha variant in children and adolescents. Methods: Between 12 January 2021 and 3 June 2021, all nucleic acid amplification tests (NAATs) of children who received a swab for SARS-CoV-2 were included. Data were collected on standardized questionnaires. The analysis of data was anonymized and retrospective. Results: We investigated 3544 NAATs; 95 children were tested positive (2.7%) for SARS-CoV-2. For the sub-analysis, 65 children were analyzed. In 59 children, the Alpha variant was found (90.8%), and 54.2% (n = 32/59) were symptomatic. The most common symptoms were fever, cough, and rhinitis. The median Ct value was 24.0 (min 17.0; max 32.7). Conclusions: We can underline early findings that children are still less effected by SARS-CoV-2 infection with the spread of the Alpha variant. We found no evidence that children infected with the Alpha variant showed more severe symptoms or suffered from a more severe clinical course than those infected with the wild type.

Comparative performance and cycle threshold values of 10 nucleic acid amplification tests for SARS-CoV-2 on clinical samples

Background A number of nucleic acid amplification tests (NAATs) for SARS-CoV-2 with different reagents have been approved for clinical use in Japan. These include research kits approved under emergency use authorization through simplified process to stabilize the supply of the reagents. Although these research kits have been increasingly used in clinical practice, limited data is available for the diagnostic performance in clinical settings. Methods We compared sensitivity, specificity, and cycle threshold (Ct) values obtained by NAATs using 10 kits approved in Japan including eight kits those receiving emergency use authorization using 69 frozen-stored clinical samples including 23 positive samples with various Ct values and 46 negative samples. Results Viral copy number of the frozen-stored samples determined with LightMix E-gene test ranged from 0.6 to 84521.1 copies/μL. While no false-positive results were obtained by any of these tests (specificity: 100% [95% CI, 88.9%-100%]), sensitivity of the nine tests ranged from 68.2% [95% CI, 45.1%-86.1%] to 95.5% [95% CI, 77.2%-99.9%] using LightMix E-gene test as the gold standard. All tests showed positive results for all samples with ≥100 copies/μL. Significant difference of Ct values even among tests amplifying the same genetic region (N1-CDC, N2) was also observed. Conclusion Difference in the diagnostic performance was observed among NAATs approved in Japan. Regarding diagnostic kits for emerging infectious diseases, a system is needed to ensure both rapidity of reagent supply and accuracy of diagnosis. Ct values, which are sometimes regarded as a marker of infectivity, are not interchangeable when obtained by different assays.