SARS-CoV-2 Detection on Artificially Contaminated Surfaces by Rapid Antigen Test

Objective: Evaluation of an antigen-based rapid test for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on artificially contaminated objects in comparison with a real-time reverse transcription-polymerase chain reaction (RT-qPCR) standard method. Materials and Methods: Artificial surface contamination with inactivated SARS-CoV-2 was tested on ten different objects comprising fruits and common materials. Three contamination levels with virus titers of 103, 104, and 105 pfu/100 μl were studied. Each object was spiked with 200 μl of virus suspension, samples were then collected by swabbing and evaluated by rapid antigen test and RT-qPCR. Additionally, 3 and 5-day contamination with SARSCoV‑2 at 105 pfu/100 μl was tested for some materials. Results: The detection rate obtained by the rapid antigen test with 103, 104, and 105 pfu/100 μl of SARS-CoV-2 was 10%, 90%, and 90%, respectively for the tested objects. RT‑qPCR showed a detection rate of 100% at all virus titers. Furthermore, both rapid antigen test and RT-qPCR were able to detect the 3 and 5-day extended contamination with SARS-CoV-2. Conclusion: The collected data suggests that the evaluated rapid antigen test is suitable for detection of SARS-CoV-2 adhered to non-human samples as a screening method. This simple method can reduce costs and turnaround time when compared to a standard molecular assay. It may be applied to enhance safety policies for COVID-19 prevention in public health and international export-businesses © All material is licensed under terms of the Creative Commons Attribution 4.0 International (CC-BY-NC-ND 4.0) license unless otherwise stated

Real-Time Monitoring of the Effectiveness of Six COVID-19 Vaccines against Laboratory-Confirmed COVID-19 in Hungary in 2021 Using the Screening Method.

Several studies have reported the waning effectiveness of COVID-19 vaccines. This study aims to demonstrate the applicability of the screening method for estimating vaccine effectiveness (VE) in a pandemic. We report VE in Hungary, estimated with the screening method, in 2021, covering a period of Alpha and the Delta variant, including the booster dose roll-out. Hungary is in a unique position to use six different vaccines in the same population. All vaccines provided a high level of protection initially, which declined over time. While the picture is different in each age group, the waning of immunity is apparent for all vaccines, especially in the younger age groups and the Sinopharm, Sputnik-V, and AstraZeneca vaccines, which performed similarly. This is clearly reversed by booster doses, more prominent for those three vaccines, where the decline in protection is more evident. Overall, two vaccines, Pfizer/BioNTech and Moderna, tend to produce the best results in all age groups, even with waning immunity considered. Using the screening method in future pandemic waves is worthwhile, especially in countries struggling with a lack of resources or when there is a need to deliver VE results within a short timeframe due to urgent decision-making.

Live-attenuated influenza vaccine effectiveness against hospitalization in children aged 2-6 years, the first three seasons of the childhood influenza vaccination program in England, 2013/14-2015/16.

INTRODUCTION: In 2013, the United Kingdom began to roll-out a universal annual influenza vaccination program for children. An important component of any new vaccination program is measuring its effectiveness. Live-attenuated influenza vaccines (LAIVs) have since shown mixed results with vaccine effectiveness (VE) varying across seasons and countries elsewhere. This study aims to assess the effectiveness of influenza vaccination in children against severe disease during the first three seasons of the LAIV program in England. METHODS: Using the screening method, LAIV vaccination coverage in children hospitalized with laboratory-confirmed influenza infection was compared with vaccination coverage in 2-6-year-olds in the general population to estimate VE in 2013/14-2015/16. RESULTS: The overall LAIV VE, adjusted for age group, week/month and geographical area, for all influenza types pooled over the three influenza seasons was 50.1% (95% confidence interval [CI] 31.2, 63.8). By age, there was evidence of protection against hospitalization from influenza vaccination in both the pre-school (2-4-year-olds) (48.1%, 95% CI 27.2, 63.1) and school-aged children (5-6-year-olds) (62.6%, 95% CI 2.6, 85.6) over the three seasons. CONCLUSION: LAIV vaccination in children provided moderate annual protection against laboratory-confirmed influenza-related hospitalization in England over the three influenza seasons. This study contributes further to the limited literature to date on influenza VE against severe disease in children.

Detection of SARS-CoV-2 infection by exhaled breath spectral analysis: Introducing a ready-to-use point-of-care mass screening method.

BACKGROUND: The current SARS-CoV-2 pandemic created an urgent need for rapid, infection screening applied to large numbers of asymptomatic individuals. To date, nasal/throat swab polymerase chain reaction (PCR) is considered the "gold standard". However, this is inconducive to mass, point-of-care (POC) testing due to person discomfort during sampling and a prolonged result turnaround. Breath testing for disease specific organic compounds potentially offers a practical, rapid, non-invasive, POC solution. The study compares the Breath of Health, Ltd. (BOH) breath analysis system to PCR's ability to screen asymptomatic individuals for SARS-CoV-2 infection. The BOH system is mobile and combines Fourier-transform infrared (FTIR) spectroscopy with artificial intelligence (AI) to generate results within 2 min and 15 s. In contrast to prior SARS-CoV-2 breath analysis research, this study focuses on diagnosing SARS-CoV-2 via disease specific spectrometric profiles rather than through identifying the disease specific molecules. METHODS: Asymptomatic emergency room patients with suspected SARS-CoV-2 exposure in two leading Israeli hospitals were selected between February through April 2021. All were tested via nasal/throat-swab PCR and BOH breath analysis. In total, 297 patients were sampled (mean age 57·08 ± SD 18·86, 156 males, 139 females, 2 unknowns). Of these, 96 were PCR-positive (44 males, 50 females, 2 unknowns), 201 were PCR-negative (112 males, 89 females). One hundred samples were used for AI identification of SARS-CoV-2 distinguishing spectroscopic wave-number patterns and diagnostic algorithm creation. Algorithm validation was tested in 100 proof-of-concept samples (34 PCR-positive, 66 PCR-negative) by comparing PCR with AI algorithm-based breath-test results determined by a blinded medical expert. One hundred additional samples (12 true PCR-positive, 85 true PCR-negative, 3 confounder false PCR-positive [not included in the 297 total samples]) were evaluated by two blinded medical experts for further algorithm validation and inter-expert correlation. FINDINGS: The BOH system identified three distinguishing wave numbers for SARS-CoV-2 infection. In the first phase, the single expert identified the first 100 samples correctly, yielding a 1:1 FTIR/AI:PCR correlation. The two-expert second-phase also yielded 1:1 FTIR/AI:PCR correlation for 97 non-confounders and null correlation for the 3 confounders. Inter-expert correlation was 1:1 for all results. In total, the FTIR/AI algorithm demonstrated 100% sensitivity and specificity for SARS-CoV-2 detection when compared with PCR. INTERPRETATION: The SARS-CoV-2 method of breath analysis via FTIR with AI-based algorithm demonstrated high PCR correlation in screening for asymptomatic individuals. This is the first practical, rapid, POC breath analysis solution with such high PCR correlation in asymptomatic individuals. Further validation is required with a larger sample size. FUNDING: Breath of Health Ltd, Rehovot, Israel provided study funding.

Rapid screening for SARS-CoV-2 VOC-Alpha (202012/01, B.1.1.7) using the Allplex™ SARS-CoV-2/FluA/FluB/RSV Assay.

BACKGROUND: The emergence of SARS-CoV-2 variants of concern (VOCs) for increased transmissibility and being potentially capable of immune-escape mandates for epidemiological surveillance. Genomic alterations present in VOCs can affect the results of RT-qPCR assays for routine diagnostic purposes, leading to peculiar profiles that can be used for rapid screening of variants. This study reports a peculiar profile observed with the Allplex™ SARS-CoV-2/FluA/FluB/RSV assay and VOC-Alpha (202012/01, lineage B.1.1.7, also named VOC-UK), which was the first identified SARS-CoV-2 VOC. METHODS: Samples were analyzed by two RT-qPCR assays: the Allplex™ SARS-CoV-2/FluA/FluB/RSV assay (ASFR, Seegene Technologies Inc; Seoul, South Korea) and the TaqPath COVID-19 RT-PCR (Thermo Fisher Scientific, USA). Definition of the SARS-CoV-2 variant was carried out by Sanger sequencing of the relevant S-gene regions and, in some cases, by whole genome sequencing (WGS) using the ARTIC-nCoV workflow on a MiniION (Oxford Nanopore Technologies, Oxford, UK) or a Illumina MiSeq platform (San Diego, California, USA). RESULTS: Of the 173 SARS-CoV-2-positive specimens, all those of lineage B.1.1.7 (N=71) showed an average Cq difference between the N and S genes of +11±2 (range, +8/+15). None of the other specimens, including several different lineages (Wild-type for the analyzed regions, N=22; Gamma, N=63; Delta, N=9; B.1.258Δ, N=3; B.1.160, N=3; B.1.177.7, N=1; B.1.1.420, N=1), exhibited a similar difference in Cq values. CONCLUSIONS: The peculiar pattern of delayed N gene positivity could constitute a convenient method for VOC-Alpha screening, simultaneous to viral detection, when using the Allplex™ SARS-CoV-2/FluA/FluB/RSV assay.

Lung Ultrasound in the Diagnosis of COVID-19 Pneumonia: Not Always and Not Only What Is COVID-19 "Glitters".

Background: In the current coronavirus disease-2019 (COVID-19) pandemic, lung ultrasound (LUS) has been extensively employed to evaluate lung involvement and proposed as a useful screening tool for early diagnosis in the emergency department (ED), prehospitalization triage, and treatment monitoring of COVID-19 pneumonia. However, the actual effectiveness of LUS in characterizing lung involvement in COVID-19 is still unclear. Our aim was to evaluate LUS diagnostic performance in assessing or ruling out COVID-19 pneumonia when compared with chest CT (gold standard) in a population of SARS-CoV-2-infected patients. Methods: A total of 260 consecutive RT-PCR confirmed SARS-CoV-2-infected patients were included in the study. All the patients underwent both chest CT scan and concurrent LUS at admission, within the first 6-12 h of hospital stay. Results: Chest CT scan was considered positive when showing a "typical" or "indeterminate" pattern for COVID-19, according to the RSNA classification system. Disease prevalence for COVID-19 pneumonia was 90.77%. LUS demonstrated a sensitivity of 56.78% in detecting lung alteration. The concordance rate for the assessment of abnormalities by both methods increased in the case of peripheral distribution and middle-lower lung location of lesions and in cases of more severe lung involvement. A total of nine patients had a "false-positive" LUS examination. Alternative diagnosis included chronic heart disease (six cases), bronchiectasis (two cases), and subpleural emphysema (one case). LUS specificity was 62.50%. Collateral findings indicative of overlapping conditions at chest CT were recorded also in patients with COVID-19 pneumonia and appeared distributed with increasing frequency passing from the group with mild disease (17 cases) to that with severe disease (40 cases). Conclusions: LUS does not seem to be an adequate tool for screening purposes in the ED, due to the risk of missing some lesions and/or to underestimate the actual extent of the disease. Furthermore, the not specificity of LUS implies the possibility to erroneously classify pre-existing or overlapping conditions as COVID-19 pneumonia. It seems more safe to integrate a positive LUS examination with clinical, epidemiological, laboratory, and radiologic findings to suggest a "virosis." Viral testing confirmation is always required.

Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR.

Since January 2021, the diffusion of the most propagated SARS-CoV-2 variants in France (UK variant 20I/501Y.V1 (lineage B.1.1.7), 20H/H501Y.V2 (lineage B.1.351) and 20J/H501Y.V3 (lineage P.1)) were urgently screened, needing a surveillance with an RT-PCR screening assay. In this study, we evaluated one RT-PCR kit for this screening (ID SARS-CoV-2/UK/SA Variant Triplex®, ID Solutions, Grabels, France) on 2207 nasopharyngeal samples that were positive for SARS-CoV-2. Using ID Solutions kit, 4.1% (92/2207) of samples were suspected to belonged to B.1.351 or P.1 variants. Next-generation sequencing that was performed on 67.4% (62/92) of these samples confirmed the presence of a B.1.351 variant in only 75.8% of the samples (47/62). Thirteen samples belonged to the UK variant (B.1.1.7), and two to A.27 with N501Y mutation. The thirteen with the UK variant presented one mutation in the S-gene, near the ΔH69/ΔV70 deletion (S71F or A67S), which impacted the detection of ΔH69/ΔV70 deletion. Using another screening kit (PKampVariantDetect SARS-CoV-2 RT-PCR combination 1 and 3® PerkinElmer, Waltham, MA, USA) on the misidentified samples, we observed that the two mutations, S71F or A67S, did not impact the detection of the UK variant. In conclusion, this study highlights the limitations of the screening strategy based on the detection of few mutations/deletions as well as it not being able to follow the virus evolution.