Diagnostic Testing for SARS-CoV-2 Infection

Investigation of Limitations in the Detection of Antibody + Antigen Complexes Using the Silicon-on-Insulator Field-Effect Transistor Biosensor

The SOI-FET biosensor (silicon-on-insulator field-effect transistor) for virus detection is a promising device in the fields of medicine, virology, biotechnology, and the environment. However, the applications of modern biosensors face numerous problems and require improvement. Some of these problems can be attributed to sensor design, while others can be attributed to technological limitations. The aim of this work is to conduct a theoretical investigation of the "antibody + antigen" complex (AB + AG) detection processes of a SOI-FET biosensor, which may also solve some of the aforementioned problems. Our investigation concentrates on the analysis of the probability of AB + AG complex detection and evaluation. Poisson probability density distribution was used to estimate the probability of the adsorption of the target molecules on the biosensor's surface and, consequently, to obtain correct detection results. Many implicit and unexpected causes of error detection have been identified for AB + AG complexes using SOI-FET biosensors. We showed that accuracy and time of detection depend on the number of SOI-FET biosensors on a crystal.

Combined Use of RT-qPCR and NGS for Identification and Surveillance of SARS-CoV-2 Variants of Concern in Residual Clinical Laboratory Samples in Miami-Dade County, Florida

Over the course of the COVID-19 pandemic, SARS-CoV-2 variants of concern (VOCs) with increased transmissibility and immune escape capabilities, such as Delta and Omicron, have triggered waves of new COVID-19 infections worldwide, and Omicron subvariants continue to represent a global health concern. Tracking the prevalence and dynamics of VOCs has clinical and epidemiological significance and is essential for modeling the progression and evolution of the COVID-19 pandemic. Next generation sequencing (NGS) is recognized as the gold standard for genomic characterization of SARS-CoV-2 variants, but it is labor and cost intensive and not amenable to rapid lineage identification. Here we describe a two-pronged approach for rapid, cost-effective surveillance of SARS-CoV-2 VOCs by combining reverse-transcriptase quantitative polymerase chain reaction (RT-qPCR) and periodic NGS with the ARTIC sequencing method. Variant surveillance by RT-qPCR included the commercially available TaqPath COVID-19 Combo Kit to track S-gene target failure (SGTF) associated with the spike protein deletion H69-V70, as well as two internally designed and validated RT-qPCR assays targeting two N-terminal-domain (NTD) spike gene deletions, NTD156-7 and NTD25-7. The NTD156-7 RT-qPCR assay facilitated tracking of the Delta variant, while the NTD25-7 RT-qPCR assay was used for tracking Omicron variants, including the BA.2, BA.4, and BA.5 lineages. In silico validation of the NTD156-7 and NTD25-7 primers and probes compared with publicly available SARS-CoV-2 genome databases showed low variability in regions corresponding to oligonucleotide binding sites. Similarly, in vitro validation with NGS-confirmed samples showed excellent correlation. RT-qPCR assays allow for near-real-time monitoring of circulating and emerging variants allowing for ongoing surveillance of variant dynamics in a local population. By performing periodic sequencing of variant surveillance by RT-qPCR methods, we were able to provide ongoing validation of the results obtained by RT-qPCR screening. Rapid SARS-CoV-2 variant identification and surveillance by this combined approach served to inform clinical decisions in a timely manner and permitted better utilization of sequencing resources.

The significance of advanced COVID-19 diagnostic testing in pandemic control measures

During the 2 years since the start of the novel coronavirus disease 2019 (COVID-19) pandemic, the scientific world made an enormous effort to fight against this disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has high transmissibility. Advancements in vaccine and treatment strategies have reduced both the hospitalization and mortality rates. However, the virus has shown its ability to evolve and evade from our COVID-19 combating armamentaria by the most common evolution mechanism—mutation. Diagnostic testing has been the first line of defense following the identification of the causative agent. Ever since, the scientific community has developed nuclei acid-based, antigen-based, and antibody-based diagnostic tests, and these testing methodologies are still playing a central role in slowing down viral transmission. These testing methods have different sensitivity and specificity and could be optimally used in areas facing different challenges owing to different level and conditions of COVID-19 outbreak. In this review, we discuss these testing methodologies as well as the considerations on how to apply these diagnostic tests optimally in the community to cope with the ever-changing pandemic conditions.

COVID-19 related maternal mortality cases in associated with Delta and Omicron waves and the role of lung ultrasound

Objective

To present coronavirus disease-2019 (COVID-19) related maternal mortality in relation to Delta and Omicron waves and to investigate the role of lung ultrasound (LUS) in estimating mortality.

Materials and Methods

This retrospective cohort study was conducted in the obstetrics and gynecology clinic of a tertiary pandemic hospital between March 2020 and January 2022. The hospitalized pregnant women with COVID-19 diagnosis and maternal deaths were studied in relation with Delta and Omicron waves. The relationship between LUS scores of hospitalized patients and maternal mortality was explored.

Results

Thousand and sixty-five pregnant women were hospitalized because of COVID-19 infection. Fifty-one (4.79%) of these patients had critical sickness, 96 (9.01%) of them had severe illness, 62 (5.82%) of them were admitted to the intensive care unit and 28 (2.63%) of all hospitalized pregnant women had died. Of the 1.065 patients, 783 (73.5%) were hospitalized before the Delta wave and the maternal mortality rate was 1.28% (10/783), 243 (22.8%) were hospitalized during the Delta wave and the maternal mortality rate was 7% (17/243) [relative risk (RR)=5.478, 95% confidence interval (CI) (2.54-11.8), z=4.342, p<0.001]. During the Omicron wave 39 (3.66%) patients were hospitalized and the maternal mortality rate was 2.56% (1/39). Maternal mortality rates, according to LUS scores, were 0.37% (1/273) for LUS 0, 0.72% (2/277) for LUS 1, 2.58% (10/387) for LUS 2 and 11.72% (15/128) for LUS 3 respectively (LUS 3 vs. others; maternal mortality: RR=8.447, 95% CI (4.11-17.34), z=5.814, p<0.0001). There were no vaccinated patients in the study cohort.

Conclusion

The maternal mortality rate was relatively high, particularly during the Delta wave at our referral center. The Delta wave, delayed vaccination and vaccine hesitancy of pregnant women might have important roles in maternal mortality. Higher LUS scores should warn clinicians of an increased risk of maternal death.

SARS-CoV-2 Transmission Control Measures in the Emergency Department: The Role of Rapid Antigenic Testing in Asymptomatic Subjects

Limiting transmission of SARS-CoV-2 from asymptomatic people assumes the paramount importance of keeping fragile subjects protected. We evaluated the utility of rapid SARS-CoV-2 antigen testing in asymptomatic subjects attending emergency departments in non-COVID-19 areas, using a single nasopharyngeal swab specimen collected in universal transport medium to perform both rapid antigen testing and rRT-PCR (used as reference standard) in a cohort of 899 patients. In the overall sample, the rapid antigen test had 43.9% sensitivity, 100% specificity, 100% positive predictive value, 93.6% negative predictive value. Considering subjects with rRT-PCR cycle threshold ≤30, the test had 80.4% sensitivity, 100% specificity, 100% positive predictive value, 98.8% negative predictive value. Considering subjects with rRT-PCR cycle threshold ≤25, the test had 94.7% sensitivity, 100% specificity, 100% positive predictive value and 99.7% negative predictive value. Despite low sensitivity, routine application of rapid antigen testing in the emergency department can lead to isolation in less than 30 min of about a half of asymptomatic COVID-19 subjects assigned to non-COVID-19 areas by clinical triage. The rapid test correctly identified 94.7% of asymptomatic patients with cycle threshold ≤ 25 that are supposed to be more infective; thus, it could be a useful measure to contain viral transmission in non-COVID-19 areas.

Improving Nasopharyngeal Swab Technique via Simulation for Frontline Workers

OBJECTIVES/HYPOTHESIS

Nasopharyngeal swabs currently remain the gold standard for COVID-19 sample collection. A surge in testing volume has resulted in a large number of health care workers who are unfamiliar with nasal anatomy performing this test, which can lead to improper collection practices culminating in false-negative results and complications. Therefore, we aimed to assess the accuracy and educational potential of a realistic 3D-printed nasal swab simulator to expedite health care workers' skill acquisition.

STUDY DESIGN

Prospective pre-post interventional study.

METHODS

A nasal swab task trainer (NSTT) was developed to scale from computed tomography data with a deviated septum. Frontline workers at COVID-19 testing sites in Ontario, Canada, were recruited to use the NSTT for nasopharyngeal swab training. Integrated video recording capability allowed participants to self-evaluate procedure accuracy. A five-point Likert scale was collected regarding the NSTT's educational value and procedural fidelity.

RESULTS

Sixty-two frontline workers included in the study were primarily registered nurses (52%) or paramedics (16%). Following simulator use, self-assessed accuracy improved in 77% of all participants and 100% of participants who expressed low confidence before training. Ninety-four percent reported that the NSTT provided a complete educational experience, and 82% regarded the system as a more effective training approach than what is currently available. Eighty-one indicated that the simulator should be used at all COVID-19 testing sites, with 77% stating province-wide implementation was warranted.

CONCLUSIONS

The nasal swab task trainer is an effective educational tool that appears well-suited for improved skill acquisition in COVID-19 testing and may be useful for training other nasal swab applications.

LEVEL OF EVIDENCE

3 Laryngoscope, 133:38-42, 2023.