Validation and verification of the Abbott RealTime SARS-CoV-2 assay analytical and clinical performance

Simplifying SARS-CoV-2 wastewater-based surveillance using an automated FDA EUA assay

Wastewater-based surveillance (WBS) can track the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in communities. Laboratory methods for this testing involve labor-intensive, multi-step processes. This study assessed the feasibility of performing WBS with an off-label use of an automated commercial SARS-CoV-2 assay that had received Emergency Use Authorization for human diagnostic testing from the United States Food and Drug Administration (FDA EUA). Twenty-four-hour composite samples of primary influent wastewater from seven municipalities in New Hampshire and Vermont were collected between September 2020 and February 2021, and were centrifuged upon receipt. An aliquot of fresh supernatant was immediately tested with the Abbott m2000 RealTime SARS-CoV-2 assay (Abbott Molecular, Des Plaines, IL, USA). Corresponding aliquots were then stored at -80°C until they were thawed, polyethylene glycol (PEG) concentrated, and tested by two PCR-based laboratory-developed tests (LDTs). Wastewater samples (103) were tested with successful detection of SARS-CoV-2 viral RNA by all three methods. Bland-Altman analysis showed overall concordant results with a bias of -0.13 and -0.42 log copies/mL detected by the FDA EUA assay compared to the LDTs. Specimen stability assessment demonstrated a decrease of 33.9% measurable viral RNA after three freeze-thaw cycles. SARS-CoV-2 detection in wastewater using an FDA EUA assay on an automated commercial testing platform performed comparably but with more efficient workflow when compared to two LDTs. This sample-to-answer automated method could save time and labor for surveillance testing, but further validation of its ability to quantitate SARS-CoV-2 viral RNA is necessary.IMPORTANCEThis proof-of-principle study evaluates an off-label use of an automated United States Food and Drug Administration (FDA) Emergency Use Authorization (EUA) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) human diagnostic assay for wastewater surveillance. Compared to standard, labor-intensive, multi-step methods currently in use for wastewater surveillance testing, an off-label use of an FDA EUA assay on an automated platform offers a sample-to-answer testing requiring less labor and a faster turnaround time.

COMPARISON OF ABBOTT REAL TIME SARS-COV-2 ASSAY AND LIFERIVER NOVEL CORONAVIRUS REAL TIME MULTIPLEX KIT FOR THE RT-PCR BASED DETECTION OF SARS-COV-2 FROM NASOPHARYNGEAL SWABS

The objective of this study was to compare performance of two authorized tests, the Abbott Real Time SARS-CoV-2 (ACOV) assay (Abbott Molecular Inc., North Chicago, IL, USA) and Liferiver Novel Coronavirus Real Time Multiplex RT-PCR (Liferiver 2019-nCoV) kit (BioVendor Group, Brno, Czech Republic), and to determine whether the selection of targeted genes has an impact on test specificity. We included 105 nasopharyngeal swabs from adult individuals with symptoms or suspected of coronavirus disease 2019 (COVID-19), aged from 26 to 91 years, previously tested by the ACOV and subsequently tested by the Liferiver 2019-nCoV. In this comparative analysis, we found that the ACOV assay detected more cases of COVID-19 infection than the Liferiver 2019-nCoV assay. The Liferiver 2019-nCoV kit showed a high level of agreement with the ACOV assay. The positive percent agreement was 88.89% (95% confidence intervals (95% CI): 77.42%-100.0%), and the kappa coefficient (kappa) was 0.901 (95% CI: 0.817-0.985). The negative percent agreement was 94.12% (95% CI: 89.74%-98.50%), while 4.76% of SARS-CoV-2 cases were false-negative using the Liferiver test. However, due to the possible false-negative results using the Liferiver 2019-nCOV test, we recommend complete testing with the ACOV assay.

Impact of SARS-CoV-2 Resistance to Antiviral Monoclonal Antibody Therapy on Neutralizing Antibody Response

Background

Anti-SARS-CoV-2 monoclonal antibodies (mAbs) have played a key role as an anti-viral against SARS-CoV-2, but there is a potential for resistance to develop. The interplay between host antibody responses and the development of monoclonal antibody (mAb) resistance is a critical area of investigation. In this study, we assessed host neutralizing antibody (nAb) responses against both ancestral virus and those with treatment-emergent E484K bamlanivimab resistance mutations.

Methods

Study participants were enrolled in the ACTIV-2/Advancing Clinical Therapeutics Globally (ACTG) A5401 phase 2 randomized, placebo-controlled trial of bamlanivimab 700 mg mAb therapy (NCT04518410). Anterior nasal and nasopharyngeal swabs were collected for SARS-CoV-2 RNA testing and S gene next-generation sequencing to identify the E484K bamlanivimab resistance mutation. Serum nAb titers were assessed by pseudovirus neutralization assays.

Results

Higher baseline (pre-treatment) nAb titers against either ancestral or E484K virus was associated with lower baseline viral load. Participants with emerging resistance had low levels of nAb titers against either ancestral or E484K nAb at the time of study entry. Participants with emergent E484K resistance developed significantly higher levels of E484K-specific nAb titers compared to mAb-treated individuals who did not develop resistance. All participants who developed the E484K mAb resistance mutation were eventually able to clear the virus.

Conclusion

Emerging drug resistance after SARS-CoV-2-specific mAb therapy led to a heightened host neutralizing antibody response to the mAb-resistant variant that was associated with eventual viral clearance. This demonstrates the interplay between the antiviral treatment-directed viral evolution and subsequent host immune response in viral clearance.

Characterization of Treatment Resistance and Viral Kinetics in the Setting of Single-Active Versus Dual-Active Monoclonal Antibodies Against Severe Acute Respiratory Syndrome Coronavirus 2

BACKGROUND

Monoclonal antibodies (mAbs) represent a crucial antiviral strategy for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, but it is unclear whether combination mAbs offer a benefit over single-active mAb treatment. Amubarvimab and romlusevimab significantly reduced the risk of hospitalizations or death in the ACTIV-2/A5401 trial. Certain SARS-CoV-2 variants are intrinsically resistant against romlusevimab, leading to only single-active mAb therapy with amubarvimab in these variants. We evaluated virologic outcomes in individuals treated with single- versus dual-active mAbs.

METHODS

Participants were nonhospitalized adults at higher risk of clinical progression randomized to amubarvimab plus romlusevimab or placebo. Quantitative SARS-CoV-2 RNA levels and targeted S-gene next-generation sequencing was performed on anterior nasal samples. We compared viral load kinetics and resistance emergence between individuals treated with effective single- versus dual-active mAbs depending on the infecting variant.

RESULTS

Study participants receiving single- or dual-active mAbs had similar demographics, baseline nasal viral load, symptom score, and symptom duration. Compared with single-active mAb treatment, treatment with dual-active mAbs led to faster viral load decline at study days 3 (P < .001) and 7 (P < .01). Treatment-emergent resistance mutations were more likely to be detected after amubarvimab plus romlusevimab treatment than with placebo (2.6% vs 0%; P < .001) and were more frequently detected in the setting of single-active compared with dual-active mAb treatment (7.3% vs 1.1%; P < .01). Single-active and dual-active mAb treatment resulted in similar decrease in rates of hospitalizations or death.

CONCLUSIONS

Compared with single-active mAb therapy, dual-active mAbs led to similar clinical outcomes but significantly faster viral load decline and a lower risk of emergent resistance.

External quality assurance in the era of standardization

Metrology in clinical chemistry aims to ensure the equivalence of measurement results from different in-vitro diagnostic measurement devices (IVD MD) for use in healthcare. The metrological traceability of measurement results to higher-order references is the cornerstone to achieving equivalent results. However, other fundamentals are also needed, including the commutability of reference materials and external quality assessment (EQA) materials for monitoring the equivalence of measurement results at the end-user level. This manuscript summarizes the findings and opinions expressed at the Joint Community for Traceability in Laboratory Medicine (JCTLM) workshop held on December 4-5, 2023. The workshop explored the relationship between EQA/proficiency testing and metrological traceability to higher-order references. EQA monitors the equivalence of measurement results from end-user IVD MDs. The workshop discussed the role and challenges of using EQA to improve and maintain the equivalence of measurement results. It also elucidated current developments in establishing the clinical suitability of laboratory results expressed as analytical performance specifications (APS).

Assessment of the clinical and analytical performance of three Seegene Allplex SARS-CoV-2 assays within the VALCOR framework

The coronavirus disease 2019 (COVID-19) pandemic demonstrated the need for accurate diagnostic testing for the early detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although the pandemic has ended, accurate assays are still needed to monitor viral spread at national levels and beyond through population and wastewater surveillance. To enhance early detection, SARS-CoV-2 assays should have high diagnostic accuracy and should be validated to assure accurate results. Three distinct SARS-CoV-2 assays were evaluated with clinical samples using the VALCOR (VALidation of SARS-CORona Virus-2 assays) framework, with the TaqPath COVID-19 assay (ThermoFisher Scientific, USA) as a comparator. We evaluated clinical sensitivity, specificity, limit of detection (LOD), and overall concordance between comparator and three index Allplex SARS-CoV-2 assays (Seegene, South Korea): Allplex-SC2, Allplex-SC2Fast (Fast PCR), and Allplex-SC2FabR (SARS-CoV-2/FluA/FluB/respiratory syncytial virus). Analytical performance and LOD of index assays were assessed using a dilution series of three synthetic SARS-CoV-2 sequence reference materials (RMs). Ninety SARS-CoV-2 positives and 90 SARS-CoV-2 negatives were tested. All Allplex assays had 100.0% sensitivity (95%CI = 95.9%-100.0%). Allplex-SC2 and Allplex-SC2Fast assays had 97.8% specificity (95%CI = 92.3%-99.7%) and 98.9% overall concordance [κ = 0.978 (95%CI = 0.947-1.000)]. Allplex-SC2FabR assay showed 100.0% specificity (95%CI = 95.9%-100.0%) and 100.0% overall concordance [κ = 1.000 (95%CI = 1.000-1.000)]. LOD assessment of index assays revealed detection down to 2.61 × 102 copies/mL in clinical samples, while the analytical LOD was 9.00 × 102 copies/mL. In conclusion, the evaluation of the three Seegene Allplex SARS-CoV-2 assays showed high sensitivity and specificity and an overall good assay concordance with the comparator. The assays showed low analytical LOD using RM and even a slightly lower LOD in clinical samples. Non-overlapping target gene sequences between SARS-CoV-2 assays and RMs emphasize the need for aligning targeted sequences of diagnostic assays and RMs.IMPORTANCEThe coronavirus disease 2019 pandemic has a significant impact on global public health, economies, and societies. As shown through the first phases of the pandemic, accurate and timely diagnosis is crucial for disease control, prevention, and monitoring. Though the pandemic phase of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has concluded, diagnostic assays remain in demand to monitor SARS-CoV-2 at the individual patient level, regionally, and nationally, as well as to remain an infectious disease preparedness instrument to monitor any new SARS-CoV-2 dissemination across borders using population and wastewater surveillance. The anticipation by WHO and central health care policy entities such as the Center for Disease Control, EMA, and multiple national health authorities is that SARS-CoV-2 will reside as an endemic respiratory disease for years to come. The key strategic consideration is hence shifting from combating a pandemic situation with a high number of patients to instead allowing precise diagnostics of suspected patients with the intention of correct management in a low-prevalence setting.

Evaluation of Abbott ID NOW COVID-19 POC test performance characteristics and integration in the regional health network workflows to improve health care delivery

With the recent global surge of SARS-CoV-2 Delta variant, there continues to be high demand for COVID-19 diagnostic testing. Abbott ID NOW is a rapid, CLIA-waived, COVID-19 diagnostic test ideally suited for use in urgent care settings or where access to diagnostic testing is limited. In this study we describe the results of rigorous validation of ID NOW and post-implementation study of POC test utilization patterns within community hospitals and clinics. Performance of ID NOW was validated by comparison of the results from 207 consecutive, paired, specimens tested on the ID NOW and on the m2000/Alinity m platforms. Once validated, ID NOW devices were placed for clinical use at four regional hospitals and clinics. We found that the ID NOW and m2000/Alinity m positive and negative percent agreement were 94.5% (95% CI, 85.1% to 98.1%) and 99.3% (95% CI, 96.4% to 99.9%), respectively. As of August 2021, a total of 2,301 tests were performed by ID NOW at individual regional network sites. The population tested consisted of 55.5% White and 42.9% Black patients, with Black patients presenting predominantly in the hospitals, while White patients were more evenly distributed between hospital and clinic sites. Disease prevalence observed among patients tested by ID NOW (12.3%) was aligned with overall prevalence seen at regional sites (11.3%). In summary, the ID NOW test can provide rapid and accurate results in a variety of near-to-patient and POC settings. If used correctly, it could serve as a valuable diagnostic tool to enable equal access to care and improve healthcare delivery within large health network systems.

Diagnostics and analysis of SARS-CoV-2: current status, recent advances, challenges and perspectives

The disastrous spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has induced severe public healthcare issues and weakened the global economy significantly. Although SARS-CoV-2 infection is not as fatal as the initial outbreak, many infected victims suffer from long COVID. Therefore, rapid and large-scale testing is critical in managing patients and alleviating its transmission. Herein, we review the recent advances in techniques to detect SARS-CoV-2. The sensing principles are detailed together with their application domains and analytical performances. In addition, the advantages and limits of each method are discussed and analyzed. Besides molecular diagnostics and antigen and antibody tests, we also review neutralizing antibodies and emerging SARS-CoV-2 variants. Further, the characteristics of the mutational locations in the different variants with epidemiological features are summarized. Finally, the challenges and possible strategies are prospected to develop new assays to meet different diagnostic needs. Thus, this comprehensive and systematic review of SARS-CoV-2 detection technologies may provide insightful guidance and direction for developing tools for the diagnosis and analysis of SARS-CoV-2 to support public healthcare and effective long-term pandemic management and control.

Contribution of PEPFAR-Supported HIV and TB Molecular Diagnostic Networks to COVID-19 Testing Preparedness in 16 Countries

The US President's Emergency Plan for AIDS Relief (PEPFAR) supports molecular HIV and tuberculosis diagnostic networks and information management systems in low- and middle-income countries. We describe how national programs leveraged these PEPFAR-supported laboratory resources for SARS-CoV-2 testing during the COVID-19 pandemic. We sent a spreadsheet template consisting of 46 indicators for assessing the use of PEPFAR-supported diagnostic networks for COVID-19 pandemic response activities during April 1, 2020, to March 31, 2021, to 27 PEPFAR-supported countries or regions. A total of 109 PEPFAR-supported centralized HIV viral load and early infant diagnosis laboratories and 138 decentralized HIV and TB sites reported performing SARS-CoV-2 testing in 16 countries. Together, these sites contributed to >3.4 million SARS-CoV-2 tests during the 1-year period. Our findings illustrate that PEPFAR-supported diagnostic networks provided a wide range of resources to respond to emergency COVID-19 diagnostic testing in 16 low- and middle-income countries.

Performances of four Nucleic Acid Amplification Tests for the identification of SARS-CoV-2 in Ethiopia

Since Coronavirus Disease-2019 (COVID-19) outbreak was reported, many commercial Nucleic Acid Amplification Tests (NAAT) have been developed all over the world, and it has been the standard method. Even though several assays were rapidly developed and applied to laboratory diagnostic testing, the performance of these assays was not evaluated in different contexts. Thus, this study aimed to assess the performance of Abbott SARS-CoV-2, Daan Gene, BGI and Sansure Biotech assays by using Composite Reference Standard (CRS). The study was conducted at the Ethiopian Public Health Institute (EPHI) from December 1 to 30/2020. Of the 164 nasopharyngeal samples were extracted by using a QIAamp RNA mini kit and Abbott DNA sample preparation system. Out of 164 samples, 59.1% were positive and 40.9% were negative by CRS. Sansure Biotech positivity was significantly low compared to CRS (p < 0.05). The overall agreement of the four assays compared to CRS was 96.3-100%. The performance of the four assays had almost comparable diagnostic performance, except for a low positive rate of Sansure Biotech assay. Hence, Sansure Biotech assay [Research Use Only (RUO)] needs further verification on its use in Ethiopia. Finally an additional study should be considered for evaluating assays with respective manufacturer claims.

Emergence of SARS-CoV-2 escape mutations during Bamlanivimab therapy in a phase II randomized clinical trial

SARS-CoV-2 mutations that cause resistance to monoclonal antibody (mAb) therapy have been reported. However, it remains unclear whether in vivo emergence of SARS-CoV-2 resistance mutations alters viral replication dynamics or therapeutic efficacy in the immune-competent population. As part of the ACTIV-2/A5401 randomized clinical trial (NCT04518410), non-hospitalized participants with symptomatic SARS-CoV-2 infection were given bamlanivimab (700 mg or 7,000 mg) or placebo treatment. Here¸ we report that treatment-emergent resistance mutations [detected through targeted Spike (S) gene next-generation sequencing] were significantly more likely to be detected after bamlanivimab 700 mg treatment compared with the placebo group (7% of 111 vs 0% of 112 participants, P = 0.003). No treatment-emergent resistance mutations among the 48 participants who received 7,000 mg bamlanivimab were recorded. Participants in which emerging mAb resistant virus mutations were identified showed significantly higher pretreatment nasopharyngeal and anterior nasal viral loads. Daily respiratory tract viral sampling through study day 14 showed the dynamic nature of in vivo SARS-CoV-2 infection and indicated a rapid and sustained viral rebound after the emergence of resistance mutations. Participants with emerging bamlanivimab resistance often accumulated additional polymorphisms found in current variants of concern/interest that are associated with immune escape. These results highlight the potential for rapid emergence of resistance during mAb monotherapy treatment that results in prolonged high-level respiratory tract viral loads. Assessment of viral resistance should be prioritized during the development and clinical implementation of antiviral treatments for COVID-19.

Clinical Performance Characteristics of the Swift Normalase Amplicon Panel for Sensitive Recovery of Severe Acute Respiratory Syndrome Coronavirus 2 Genomes

Amplicon-based sequencing methods are central in characterizing the diversity, transmission, and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but need to be rigorously assessed for clinical utility. Herein, we validated the Swift Biosciences' SARS-CoV-2 Swift Normalase Amplicon Panels using remnant clinical specimens. High-quality genomes meeting our established library and sequence quality criteria were recovered from positive specimens, with 95% limit of detection of 40.08 SARS-CoV-2 copies/PCR. Breadth of genome recovery was evaluated across a range of CT values (11.3 to 36.7; median, 21.6). Of 428 positive samples, 413 (96.5%) generated genomes with <10% unknown bases, with a mean genome coverage of 13,545× ± SD 8382×. No genomes were recovered from PCR-negative specimens (n = 30) or from specimens positive for non-SARS-CoV-2 respiratory viruses (n = 20). Compared with whole-genome shotgun metagenomic sequencing (n = 14) or Sanger sequencing for the spike gene (n = 11), pairwise identity between consensus sequences was 100% in all cases, with highly concordant allele frequencies (R2 = 0.99) between Swift and shotgun libraries. When samples from different clades were mixed at varying ratios, expected variants were detected even in 1:99 mixtures. When deployed as a clinical test, 268 tests were performed in the first 23 weeks, with a median turnaround time of 11 days, ordered primarily for outbreak investigations and infection control.

Antiviral and clinical activity of bamlanivimab in a randomized trial of non-hospitalized adults with COVID-19

Anti-SARS-CoV-2 monoclonal antibodies are mainstay COVID-19 therapeutics. Safety, antiviral, and clinical efficacy of bamlanivimab were evaluated in the randomized controlled trial ACTIV-2/A5401. Non-hospitalized adults were randomized 1:1 within 10 days of COVID-19 symptoms to bamlanivimab or blinded-placebo in two dose-cohorts (7000 mg, n = 94; 700 mg, n = 223). No differences in bamlanivimab vs placebo were observed in the primary outcomes: proportion with undetectable nasopharyngeal SARS-CoV-2 RNA at days 3, 7, 14, 21, and 28 (risk ratio = 0.82-1.05 for 7000 mg [p(overall) = 0.88] and 0.81-1.21 for 700 mg [p(overall) = 0.49]), time to symptom improvement (median 21 vs 18.5 days [p = 0.97], 7000 mg; 24 vs 20.5 days [p = 0.08], 700 mg), or grade 3+ adverse events. However, bamlanivimab was associated with lower day 3 nasopharyngeal viral levels and faster reductions in inflammatory markers and viral decay by modeling. This study provides evidence of faster reductions in nasopharyngeal SARS-CoV-2 RNA levels but not shorter symptom durations in non-hospitalized adults with early variants of SARS-CoV-2.

Viral and Symptom Rebound in Untreated COVID-19 Infection

Background

There are reports of viral RNA and symptom rebound in people with COVID-19 treated with nirmatrelvir/ritonavir. Since the natural course of viral and symptom trajectories of COVID-19 has not been well described, we evaluated the incidence of viral and symptom rebound in untreated outpatients with mild-moderate COVID-19.

Methods

The study population included 568 participants enrolled in the ACTIV-2/A5401 platform trial who received placebo. Anterior nasal swabs were collected for SARS-CoV-2 RNA testing on days 0-14, 21 and 28. Participants recorded the severity of 13 targeted symptoms daily from day 0 to 28. Viral rebound was defined as ≥0.5 log10 viral RNA copies/mL increase and symptom rebound was defined as a 4-point total symptom score increase from baseline. Baseline was defined as study day 4 (primary analysis) or 8 days from symptom onset (secondary analysis).

Findings

In both the primary and secondary analyses, 12% of participants had viral rebound. Viral rebounders were older than non-rebounders (median 54 vs 47 years, P=0.04). Symptom rebound occurred in 27% of participants after initial symptom improvement and in 10% of participants after initial symptom resolution. The combination of high-level viral rebound to ≥5.0 log10 RNA copies/mL and symptom rebound after initial improvement was observed in 1-2% of participants.

Interpretation

Viral RNA rebound or symptom relapse in the absence of antiviral treatment is common, but the combination of high-level viral and symptom rebound is rare.

Cycle threshold values and SARS-CoV-2: Relationship to demographic characteristics and disease severity

Cycle threshold (Ct), or the number of cycles required to amplify viral RNA to a detectable level, provides an estimate of viral load. Previous studies have demonstrated mixed results in regard to the association between SARS-CoV-2 Ct from real-time reverse transcriptase PCR (rRT-PCR) testing to patient outcomes, and there is less data on the relationship between Ct and patient characteristics. This was a retrospective study of 256 patients tested at a tertiary care emergency department from March to July 2020 via nasopharyngeal rRT-PCR testing utilizing the Abbott M2000 SARS-CoV-2 assay. Kruskal-Wallis, univariable, and multivariable logistic regression were used where appropriate for analysis. There were no significant differences in Ct value by demographic characteristics including age, sex, race, or ethnicity. Ct increased with time since symptom onset (p < 0.001), and increasing Ct was associated with increased odds of severe disease (odds ratio: 1.05, 95% confidence interval: 1.0-1.11). Ct was not found to be associated with patient demographic characteristics and increasing Ct was found to be associated with increased odds of severe disease. Continued study will allow us to better comprehend the complex factors that contribute to the risk for severe outcomes due to SARS-CoV-2 infection.

Strategies for Scaling up SARS-CoV-2 Molecular Testing Capacity

Scaling up SARS-CoV-2 testing during the COVID-19 pandemic was critical to maintaining clinical operations and an open society. Pooled testing and automation were two critical strategies used by laboratories to meet the unprecedented demand. Here, we review these and other cutting-edge strategies that sought to expand SARS-CoV-2 testing capacity while maintaining high individual test performance.

Clinical evaluation of the automated Abbott RealTime SARS-CoV-2, Alinity m SARS-CoV-2, and Alinity m Resp-4-Plex assays

BACKGROUND

Detection of SARS-CoV-2 infections relies on the use of sensitive, accurate and high throughput RT-PCR assays.

OBJECTIVES

We assessed the analytical performance of the Abbott RealTime SARS-CoV-2 (RT-SARS), Alinity m SARS-CoV-2 (AlinSARS) assays and compared the clinical performance of the RT-SARS, AlinSARS, and Alinity m Resp-4-Plex (Alin4Plex) assays to the Seegene Allplex assay (Allplex) and an inhouse test (Inhouse).

RESULTS

We found 100 % positive percent agreement (PPA) and 100 % negative percent agreement (NPA) comparing RT-SARS and Allplex. RT-SARS, AlinSARS and Inhouse showed 100 % NPA and 100 % PPA across all assays, except for the RdRp target of Inhouse (PPA = 84 %). Similarly, Alin4Plex and Allplex showed high agreement with specimens containing either SARS-CoV-2, influenza A, influenza B, or RSV. Detection rates of 100 % for SARS-CoV-2 at 50 copies/mL, high precision, and no cross-reactivity with non-SARS-CoV-2 respiratory pathogens were observed for RT-SARS and AlinSARS. AlinSARS detected SARS-CoV-2 in spiked throat washes and in specimens infected with SARS-CoV-2 Alpha or Beta variants.

CONCLUSIONS

The newly developed RT-SARS, AlinSARS, and Alin4Plex assays proved to be useful for detecting SARS-CoV-2 RNA in clinical samples.

SNP and Phylogenetic Characterization of Low Viral Load SARS-CoV-2 Specimens by Target Enrichment

Background: Surveillance of SARS-CoV-2 across the globe has enabled detection of new variants and informed the public health response. With highly sensitive methods like qPCR widely adopted for diagnosis, the ability to sequence and characterize specimens with low titers needs to keep pace.

Methods: Nucleic acids extracted from nasopharyngeal swabs collected from four sites in the United States in early 2020 were converted to NGS libraries to sequence SARS-CoV-2 genomes using metagenomic and xGen target enrichment approaches. Single nucleotide polymorphism (SNP) analysis and phylogeny were used to determine clade assignments and geographic origins of strains.

Results: SARS-CoV-2-specific xGen enrichment enabled full genome coverage for 87 specimens with Ct values &lt;29, corresponding to viral loads of &gt;10,000 cp/ml. For samples with viral loads between 103 and 106 cp/ml, the median genome coverage for xGen was 99.1%, sequence depth was 605X, and the “on-target” rate was 57 ± 21%, compared to 13%, 2X and 0.001 ± 0.016%, respectively, for metagenomic sequencing alone. Phylogenetic analysis revealed the presence of most clades that existed at the time of the study, though clade GH dominated in the Midwest.

Conclusions: Even as vaccines are being widely distributed, a high case load of SARS-CoV-2 infection persists around the world. Viral genetic surveillance has succeeded in warning the public of new variants in circulation and ensured that diagnostic tools remain resilient to a steadily increasing number of mutations. Target capture offers a means of characterizing low viral load samples which would normally pose a challenge for metagenomic sequencing.

Infection prevention strategies are highly protective in COVID-19 units while main risks to healthcare professionals come from coworkers and the community

Background

Early evaluations of healthcare professional (HCP) COVID-19 risk occurred during insufficient personal protective equipment and disproportionate testing, contributing to perceptions of high patient-care related HCP risk. We evaluated HCP COVID-19 seropositivity after accounting for community factors and coworker outbreaks.

Methods

Prior to universal masking, we conducted a single-center retrospective cohort plus cross-sectional study. All HCP (1) seen by Occupational Health for COVID-like symptoms (regardless of test result) or assigned to (2) dedicated COVID-19 units, (3) units with a COVID-19 HCP outbreak, or (4) control units from 01/01/2020 to 04/15/2020 were offered serologic testing by an FDA-authorized assay plus a research assay against 67 respiratory viruses, including 11 SARS-CoV-2 antigens. Multivariable models assessed the association of demographics, job role, comorbidities, care of a COVID-19 patient, and geocoded socioeconomic status with positive serology.

Results

Of 654 participants, 87 (13.3%) were seropositive; among these 60.8% (N = 52) had never cared for a COVID-19 patient. Being male (OR 1.79, CI 1.05–3.04, p = 0.03), working in a unit with a HCP-outbreak unit (OR 2.21, CI 1.28–3.81, p < 0.01), living in a community with low owner-occupied housing (OR = 1.63, CI = 1.00–2.64, p = 0.05), and ethnically Latino (OR 2.10, CI 1.12–3.96, p = 0.02) were positively-associated with COVID-19 seropositivity, while working in dedicated COVID-19 units was negatively-associated (OR 0.53, CI = 0.30–0.94, p = 0.03). The research assay identified 25 additional seropositive individuals (78 [12%] vs. 53 [8%], p < 0.01).

Conclusions

Prior to universal masking, HCP COVID-19 risk was dominated by workplace and community exposures while working in a dedicated COVID-19 unit was protective, suggesting that infection prevention protocols prevent patient-to-HCP transmission.

Article summary

Prior to universal masking, HCP COVID-19 risk was dominated by workplace and community exposures while working in a dedicated COVID-19 unit was protective, suggesting that infection prevention protocols prevent patient-to-HCP transmission.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13756-021-01031-5.

SARS-CoV-2 could be spread through hospital medication dispensed to patients: A prospective observational study

ABSTRACT

Our objective was to analyze in vitro the persistence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in the packaging material of the drugs dispensed to hospital wards. Additionally, to evaluate if the protection with a double plastic bag prevents the contamination of the medication dispensed to an intensive care unit (ICU).On the first part, different materials containing different drugs within an ICU were sampled to confirm the lack of contamination by SARS-CoV-2. The confirmation of the virus was performed using real time reverse transcription polymerase chain reaction. As a control group, in the microbiology laboratory we inoculated the virus into the different surfaces containing the same drugs included in the first part. Samples were obtained with a sterile swab at 3, 6, 8, 10, 14, 21, and 30 days after inoculation and analyzed through real time reverse transcription polymerase chain reaction.None of the studied materials containing the drugs within an ICU was contaminated by SARS-CoV-2. In the second part, SARS-CoV-2 was found in all surfaces for up to 30 days.The use of double-bag unit-dose system to deliver medication in a pandemic seems effective to prevent the potential transmission of SARS-CoV-2. A striking SARS-CoV-2 RNA stability of up to 30 days was found in the surfaces containing the drugs.

Development of the RealTime SARS-CoV-2 quantitative Laboratory Developed Test and correlation with viral culture as a measure of infectivity

While diagnosis of COVID-19 relies on qualitative molecular testing for the absence or presence of SARS-CoV-2 RNA, quantitative viral load determination for SARS-CoV-2 has many potential applications in antiviral therapy and vaccine trials as well as implications for public health and quarantine guidance. To date, no quantitative SARS-CoV-2 viral load tests have been authorized for clinical use by the FDA. In this study, we modified the FDA emergency use authorized qualitative RealTime SARS-CoV-2 assay into a quantitative SARS-CoV-2 Laboratory Developed Test (LDT) using newly developed Abbott SARS-CoV-2 calibration standards. Both analytical and clinical performance of this SARS-CoV-2 quantitative LDT was evaluated using nasopharyngeal swabs (NPS). We further assessed the correlation between Ct and the ability to culture virus on Vero CCL81 cells. The SARS-CoV-2 quantitative LDT demonstrated high linearity with R2 value of 0.992, high inter- and intra-assay reproducibility across the dynamic range (SDs ± 0.08-0.14 log10 copies/mL for inter-assay reproducibility and ± 0.09 to 0.19 log10 copies/mL for intra-assay reproducibility). Lower limit of detection was determined as 1.90 log10 copies/mL. The highest Ct at which CPE was detected ranged between 28.21-28.49, corresponding to approximately 4.2 log10 copies/mL. Quantitative tests, validated against viral culture capacity, may allow more accurate identification of individuals with and without infectious viral shedding from the respiratory tract.

Emergence of SARS-CoV-2 Resistance with Monoclonal Antibody Therapy

Resistance mutations to monoclonal antibody (mAb) therapy has been reported, but in the non-immunosuppressed population, it is unclear if in vivo emergence of SARS-CoV-2 resistance mutations alters either viral replication dynamics or therapeutic efficacy. In ACTIV-2/A5401, non-hospitalized participants with symptomatic SARS-CoV-2 infection were randomized to bamlanivimab (700mg or 7000mg) or placebo. Treatment-emergent resistance mutations were significantly more likely detected after bamlanivimab 700mg treatment than placebo (7% of 111 vs 0% of 112 participants, P=0.003). There were no treatment-emergent resistance mutations among the 48 participants who received bamlanivimab 7000mg. Participants with emerging mAb resistant virus had significantly higher pre-treatment nasopharyngeal and anterior nasal viral load. Intensive respiratory tract viral sampling revealed the dynamic nature of SARS-CoV-2 evolution, with evidence of rapid and sustained viral rebound after emergence of resistance mutations, and worsened symptom severity. Participants with emerging bamlanivimab resistance often accumulated additional polymorphisms found in current variants of concern/interest and associated with immune escape. These results highlight the potential for rapid emergence of resistance during mAb monotherapy treatment, resulting in prolonged high level respiratory tract viral loads and clinical worsening. Careful virologic assessment should be prioritized during the development and clinical implementation of antiviral treatments for COVID-19.

Comparison of diagnostic performance of five molecular assays for detection of SARS-CoV-2

We compared the performance of the Abbott Real Time SARS-CoV-2 assay (Abbott assay), Aptima™ SARS-CoV-2 assay (Aptima assay), BGI Real-Time SARS-CoV-2 assay (BGI assay), Lyra® SARS-CoV-2 assay (Lyra assay), and DiaSorin Simplexa™ COVID assay for SARS-CoV-2 detection. Residual nasopharyngeal samples (n = 201) submitted for routine SARS-CoV-2 testing by Simplexa assay during June-July 2020 and January 2021 were salvaged. Aliquots were tested on other assays and compared against the CDC 2019-nCoV Real-Time RT-PCR assay. Viral load in positive samples was determined by droplet digital PCR. Among 201 samples, 99 were positive and 102 were negative by the CDC assay. The Aptima and Abbott assays exhibited the highest positive percent agreement (PPA) at 98.9% while the BGI assay demonstrated the lowest PPA of 89.9% with 10 missed detections. Negative percent agreement for all 5 platforms was comparable, ranging from 96.1% to 100%. The performance of all five assays was comparable.

Nasal Swab Performance by Collection Timing, Procedure, and Method of Transport for Patients with SARS-CoV-2

The urgent need for large-scale diagnostic testing for SARS-CoV-2 has prompted interest in sample collection methods of sufficient sensitivity to replace nasopharynx (NP) sampling. Nasal swab samples are an attractive alternative; however, previous studies have disagreed over how nasal sampling performs relative to NP sampling. Here, we compared nasal versus NP specimens collected by health care workers in a cohort of individuals clinically suspected of COVID-19 as well as SARS-CoV-2 reverse transcription (RT)-PCR-positive outpatients undergoing follow-up. We compared subjects being seen for initial evaluation versus follow-up, two different nasal swab collection protocols, and three different transport conditions, including traditional viral transport media (VTM) and dry swabs, on 307 total study participants. We compared categorical results and viral loads to those from standard NP swabs collected at the same time from the same patients. All testing was performed by RT-PCR on the Abbott SARS-CoV-2 RealTime emergency use authorization (EUA) (limit of detection [LoD], 100 copies viral genomic RNA/ml transport medium). We found low concordance overall, with Cohen's kappa (κ) of 0.49, with high concordance only for subjects with very high viral loads. We found medium concordance for testing at initial presentation (κ = 0.68) and very low concordance for follow-up testing (κ = 0.27). Finally, we show that previous reports of high concordance may have resulted from measurement using assays with sensitivity of ≥1,000 copies/ml. These findings suggest nasal-swab testing be used for situations in which viral load is expected to be high, as we demonstrate that nasal swab testing is likely to miss patients with low viral loads.

Reducing COVID-19 quarantine with SARS-CoV-2 testing: a simulation study

OBJECTIVE

To evaluate the effectiveness of SARS-CoV-2 testing on shortening the duration of quarantines for COVID-19 and to identify the most effective choices of testing schedules.

DESIGN

We performed extensive simulations to evaluate the performance of quarantine strategies when one or more SARS-CoV-2 tests were administered during the quarantine. Simulations were based on statistical models for the transmissibility and viral loads of SARS-CoV-2 infections and the sensitivities of available testing methods. Sensitivity analyses were performed to evaluate the impact of perturbations in model assumptions on the outcomes of optimal strategies.

RESULTS

We found that SARS-CoV-2 testing can effectively reduce the length of a quarantine without compromising safety. A single reverse transcription-PCR (RT-PCR) test performed before the end of quarantine can reduce quarantine duration to 10 days. Two tests can reduce the duration to 8 days, and three highly sensitive RT-PCR tests can justify a 6-day quarantine. More strategic testing schedules and longer quarantines are needed if tests are administered with less-sensitive RT-PCR tests or antigen tests. Shorter quarantines can be used for applications that tolerate a residual postquarantine transmission risk comparable to a 10-day quarantine.

CONCLUSIONS

Testing could substantially reduce the length of isolation, reducing the physical and mental stress caused by lengthy quarantines. With increasing capacity and lowered costs of SARS-CoV-2 tests, test-assisted quarantines could be safer and more cost-effective than 14-day quarantines and warrant more widespread use.

Tools and Techniques for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)/COVID-19 Detection

The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory disease coronavirus 2 (SARS-CoV-2), has led to millions of confirmed cases and deaths worldwide. Efficient diagnostic tools are in high demand, as rapid and large-scale testing plays a pivotal role in patient management and decelerating disease spread. This paper reviews current technologies used to detect SARS-CoV-2 in clinical laboratories as well as advances made for molecular, antigen-based, and immunological point-of-care testing, including recent developments in sensor and biosensor devices. The importance of the timing and type of specimen collection is discussed, along with factors such as disease prevalence, setting, and methods. Details of the mechanisms of action of the various methodologies are presented, along with their application span and known performance characteristics. Diagnostic imaging techniques and biomarkers are also covered, with an emphasis on their use for assessing COVID-19 or monitoring disease severity or complications. While the SARS-CoV-2 literature is rapidly evolving, this review highlights topics of interest that have occurred during the pandemic and the lessons learned throughout. Exploring a broad armamentarium of techniques for detecting SARS-CoV-2 will ensure continued diagnostic support for clinicians, public health, and infection prevention and control for this pandemic and provide advice for future pandemic preparedness.

Performance of three polymerase chain reaction-based assays for detection of SARS-CoV-2 in different upper respiratory tract specimens

To meet the testing demands and overcome supply chain issues during the SARS-CoV-2 pandemic, many clinical laboratories validated multiple SARS-CoV-2 molecular testing platforms. Here, we compare three different molecular assays for SARS-CoV-2 that received emergency use authorization (EUA) from the U.S. Food and Drug Administration. In order to determine the agreement among Roche cobas® SARS-CoV-2 Test (Cobas), Abbott RealTime SARS-CoV-2 assay (ART), and Mayo Clinic Laboratory SARS-CoV-2 Molecular Detection Assay (Mayo LDT), 100 each of anterior nares (AN), nasopharyngeal (NP), oropharyngeal (OP), and NP+OP swabs were tested on each platform. The consensus result was defined as agreement by 2 or more methods. Furthermore, 30 positive NP swabs from each molecular platform (n = 90 total) were tested on the three platforms to determine the PPA among positive samples. ART platform called more specimens positive than the other two platforms. All three assays performed with greater than 90% agreement for NP specimens throughout the study.

Review of Current COVID-19 Diagnostics and Opportunities for Further Development

Diagnostic testing plays a critical role in addressing the coronavirus disease 2019 (COVID-19) pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Rapid and accurate diagnostic tests are imperative for identifying and managing infected individuals, contact tracing, epidemiologic characterization, and public health decision making. Laboratory testing may be performed based on symptomatic presentation or for screening of asymptomatic people. Confirmation of SARS-CoV-2 infection is typically by nucleic acid amplification tests (NAAT), which requires specialized equipment and training and may be particularly challenging in resource-limited settings. NAAT may give false-negative results due to timing of sample collection relative to infection, improper sampling of respiratory specimens, inadequate preservation of samples, and technical limitations; false-positives may occur due to technical errors, particularly contamination during the manual real-time polymerase chain reaction (RT-PCR) process. Thus, clinical presentation, contact history and contemporary phyloepidemiology must be considered when interpreting results. Several sample-to-answer platforms, including high-throughput systems and Point of Care (PoC) assays, have been developed to increase testing capacity and decrease technical errors. Alternatives to RT-PCR assay, such as other RNA detection methods and antigen tests may be appropriate for certain situations, such as resource-limited settings. While sequencing is important to monitor on-going evolution of the SARS-CoV-2 genome, antibody assays are useful for epidemiologic purposes. The ever-expanding assortment of tests, with varying clinical utility, performance requirements, and limitations, merits comparative evaluation. We herein provide a comprehensive review of currently available COVID-19 diagnostics, exploring their pros and cons as well as appropriate indications. Strategies to further optimize safety, speed, and ease of SARS-CoV-2 testing without compromising accuracy are suggested. Access to scalable diagnostic tools and continued technologic advances, including machine learning and smartphone integration, will facilitate control of the current pandemic as well as preparedness for the next one.

Verification and Validation of SARS-CoV-2 Assay Performance on the Abbott m2000 and Alinity m Systems

We verified the analytical performance of the Abbott RealTime SARS-CoV-2 assay on the m2000 system and compared its clinical performance to the CDC 2019-nCoV real-time PCR diagnostic panel and the Thermo Fisher TaqPath RT-PCR COVID-19 kit. We also performed a bridging study comparing the RealTime SARS-CoV-2 assay with the new Abbott Alinity m SARS-CoV-2 assay. A number of standards, reference materials, and commercially available controls were used for the analytical verification to confirm the limit of detection, linearity, and reproducibility. We used nasopharyngeal (NP) swab specimens collected in saline for the clinical verification and bridging studies. Overall, we found 91.2% positive percent agreement (PPA; 95% confidence interval [CI] = 76.2 to 98.14%) and a 100% negative percent agreement (NPA; 95% CI = 97.97 to 100%) between the results of the RealTime SARS-CoV-2 and CDC tests with 217 NP specimens (P = 0.13). We found a PPA of 100% (95% CI = 90.26 to 100%) and an NPA of 95.15% (95% CI = 83.47 to 99.4%) between the results of the RealTime and TaqPath tests with 77 NP specimens (P = 0.24). Finally, we tested 203 NP swab specimens for SARS-CoV-2 on the m2000 on the Alinity m systems. The PPA and NPA were 92.2% (95% CI = 85.3 to 96.59%) and 92% (95% CI = 84.8 to 96.5%), respectively (P = 0.4). Although cycle number (Cn) values obtained for the concordant positive samples were highly correlated (R ² = 0.95), the Cn values were on average 14.14 higher on the Alinity m system due to the unread cycles with the RealTime SARS-CoV-2 assay.

Severe acute respiratory syndrome coronavirus 2: a canary in the coal mine for public safety net hospitals

BACKGROUND

The coronavirus disease 2019 pandemic has exposed disproportionate health inequities among underserved populations, including refugees. Public safety net healthcare systems play a critical role in facilitating access to care for refugees and informing coordinated public health prevention and mitigation efforts during a pandemic.

OBJECTIVE

This study aimed to evaluate the prevalence ratios of severe acute respiratory syndrome coronavirus 2 infection between refugee women and nonrefugee parturient patients admitted to the hospital for delivery. Here, we suspected that the burden of infection was disproportionately distributed across refugee communities that may act as sentinels for community outbreaks.

STUDY DESIGN

A cross-sectional study was conducted examining parturient women admitted to the maternity unit between May 6, 2020, and July 22, 2020, when universal testing for severe acute respiratory syndrome coronavirus 2 was first employed. Risk factors for severe acute respiratory syndrome 2 positivity were ascertained, disaggregated by refugee status, and other clinical and sociodemographic variables examined. Prevalence ratios were calculated and comparisons made to county-level community prevalence over the same period.

RESULTS

The positive test percentage at the county-level during this study period was 21.6%. Of 350 women admitted to the hospital for delivery, 33 (9.4%) tested positive for severe acute respiratory syndrome 2. When refugee status was determined, 45 women (12.8%) were identified as refugees. Of the 45 refugee women, 8 (17.8%) tested positive for severe acute respiratory syndrome 2 compared with 25 nonrefugee patients (8.19%) who tested positive for severe acute respiratory syndrome 2 (prevalence ratio, 2.16; 95% confidence interval, 1.04–4.51). In addition, 7 of the refugee women who tested positive for severe acute respiratory syndrome coronavirus 2 were from Central Africa.

CONCLUSION

The severe acute respiratory syndrome coronavirus 2 outbreak has disproportionately affected refugee populations. This study highlighted the utility of universal screening in mounting a rapid response to an evolving pandemic and how we can better serve refugee communities. Focused response may help achieve more equitable care related to severe acute respiratory syndrome 2 among vulnerable communities. The identification of such populations may help mitigate the spread of the disease and facilitate a timely, culturally, and linguistically enhanced public health response.

Assessment of SARS-CoV-2 infectivity of upper respiratory specimens from COVID-19 patients by virus isolation using VeroE6/TMPRSS2 cells

Background

An outbreak of novel coronavirus (SARS-CoV-2)-associated respiratory infectious diseases (COVID-19) emerged in 2019 and has spread rapidly in humans around the world. The demonstration of in vitro infectiousness of respiratory specimens is an informative surrogate for SARS-CoV-2 transmission from patients with COVID-19; accordingly, viral isolation assays in cell culture are an important aspect of laboratory diagnostics for COVID-19.

Methods

We developed a simple and rapid protocol for isolating SARS-CoV-2 from respiratory specimens using VeroE6/TMPRSS2 cells, a cell line that is highly susceptible to the virus. We also investigated a correlation between isolation of SARS-CoV-2 and viral load detected by real-time RT-PCR (rRT-PCR) using N2 primer/probe set that has been developed for testing of COVID-19 in Japan.

Results

The SARS-CoV-2 isolation protocol did not require blind passage of inoculated cells and yielded the results of viral isolation within 7 days after inoculation. Specimens with cycle threshold (Ct) values of <20.2, determined by rRT-PCR, were predicted to be isolation-positive. On the other hand, 6.9% of specimens with Ct values >35 were virus isolation-positive, indicating that low viral loads (high Ct values) in upper respiratory specimens do not always indicate no risk of containing transmissible virus.

Conclusion

In combination with rRT-PCR, the SARS-CoV-2 isolation protocol provides a means for assessing the potential risk of transmissible virus in upper respiratory specimens.

Identification of Presymptomatic and Asymptomatic Cases Using Cohort-Based Testing Approaches at a Large Correctional Facility-Chicago, Illinois, USA, May 2020

BACKGROUND

Coronavirus disease 2019 (COVID-19) continues to cause significant morbidity and mortality worldwide. Correctional and detention facilities are at high risk of experiencing outbreaks. We aimed to evaluate cohort-based testing among detained persons exposed to laboratory-confirmed cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in order to identify presymptomatic and asymptomatic cases.

METHODS

During 1-19 May 2020, 2 testing strategies were implemented in 12 tiers or housing units of the Cook County Jail, Chicago, Illinois. Detained persons were approached to participate in serial testing (n = 137) and offered tests at 3 time points over 14 days (day 1, days 3-5, and days 13-14). The second group was offered a single test and interview at the end of a 14-day quarantine period (day 14 group) (n = 87).

RESULTS

224 detained persons were approached for participation and, of these, 194 (87%) participated in ≥1 interview and 172 (77%) had ≥1 test. Of the 172 tested, 19 were positive for SARS-CoV-2. In the serial testing group, 17 (89%) new cases were detected, 16 (84%) on day 1, 1 (5%) on days 3-5, and none on days 13-14; in the day 14 group, 2 (11%) cases were identified. More than half (12/19; 63%) of the newly identified cases were presymptomatic or asymptomatic.

CONCLUSIONS

Our findings highlight the utility of cohort-based testing promptly after initiating quarantine within a housing tier. Cohort-based testing efforts identified new SARS-CoV-2 asymptomatic and presymptomatic infections that may have been missed by symptom screening alone.

ICAM-1 levels in patients with covid-19 with diabetic foot ulcers: A prospective study in southeast asia

BACKGROUND

Viral infection can compound the severity of pre-existing inflammation caused by underlying diseases. For those with a chronic, immune-related condition such as diabetic foot ulcers (DFUs), the coronavirus disease (COVID-19) serves to exacerbate the inflammatory burden. Serum levels of intracellular adhesion molecule-1 (ICAM-1), a primary mediator of cell adhesion express in the inflammatory process, are often used to indicate the gravity of all inflammatory conditions. Therefore, the purpose of this study was to investigate serum ICAM-1 levels before and after debridement in patients with DFUs who were also diagnosed as COVID-19 positive compared with those who were COVID-19 negative.

METHODS

20 patients with DFUs were screened for COVID-19 and then divided into COVID-19 positive and negative groups according to the results. Before debridement, chest x-rays and blood analysis, including ICAM-1 serum levels, were performed in both groups. Only ICAM-1 serum levels were measured after debridement.

RESULTS

Of the 20 patients included in this study, 55% were male (n = 11) and 45% were female (n = 9). The mean age was 52.9 ± 1.9 years. ICAM-1 levels in patients with DFU in the COVID-19-positive group were significantly higher than those in the COVID-19-negative group (median 317.2 vs 149.2, respectively; p < 0.001). Serum levels of ICAM-1 reduced significantly in patients with DFU in the COVID-19-positive group were significantly higher than those in the COVID-19-negative group after debridement (median 312.5 vs 130.3; p < 0.001).

CONCLUSION

ICAM-1 serum levels represent an additional, initial screening marker for COVID-19.

Optimal test-assisted quarantine strategies for COVID-19

Objective

To evaluate the effectiveness of SARS-CoV-2 testing on shortening the duration of quarantines for COVID-19 and to identify the most effective choices of testing schedules.

Design

We performed extensive simulations to evaluate the performance of quarantine strategies when one or more SARS-CoV-2 tests were administered during the quarantine. Simulations were based on statistical models for the transmissibility and viral loads of SARS-CoV-2 infections and the sensitivities of available testing methods. Sensitivity analyses were performed to evaluate the impact of perturbations in model assumptions on the outcomes of optimal strategies.

Results

We found that SARS-CoV-2 testing can effectively reduce the length of a quarantine without compromising safety. A single RT-PCR test performed before the end of quarantine can reduce quarantine duration to 10 days. Two tests can reduce the duration to 8 days, and three highly sensitive RT-PCR tests can justify a 6-day quarantine. More strategic testing schedules and longer quarantines are needed if tests are administered with less sensitive RT-PCR tests or antigen tests. Shorter quarantines can be utilized for applications that tolerate a residual post-quarantine transmission risk comparable to a 10-day quarantine.

Conclusions

Testing could substantially reduce the length of isolation, reducing the physical and mental stress caused by lengthy quarantines. With increasing capacity and lowered costs of SARS-CoV-2 tests, test-assisted quarantines could be safer and more cost-effective than 14-day quarantines and warrant more widespread use.

RESEARCH IN CONTEXT

What is already known on this topic?: Recommendations for quarantining individuals who could have been infected with COVID-19 are based on limited evidence.Despite recent theoretical and case studies of test-assisted quarantines, there has been no substantive investigation to quantify the safety and efficacy of, nor an exhaustive search for, optimal test-assisted quarantine strategies.

What this study adds

Our simulations indicate that the 14-day quarantine approach is overly conservative and can be safely shortened if testing is performed.Our recommendations include testing schedules that could be immediately adopted and implemented as government and industry policies.

Role of the Funding Source

A major technology company asked that we perform simulations to understand the optimal strategy for managing personnel quarantining before forming cohorts of individuals who would work closely together. The funding entity did not influence the scope or output of the study but requested that we include antigen testing as a component of the quarantining process. Patrick Yu and Peter Matos are employees of Corporate Medical Advisors, and International S.O.S employs Julie McCashin. Other funding sources are research grants and did not influence the investigation.

Analytical Sensitivity of the Abbott BinaxNOW COVID-19 Ag Card

Multiple rapid antigen (Ag) tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have recently received emergency-use authorization (EUA) from the U.S. Food and Drug Administration (FDA).

Multiple rapid antigen (Ag) tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have recently received emergency-use authorization (EUA) from the U.S. Food and Drug Administration (FDA). Although less sensitive than molecular detection methods, rapid antigen testing offers the potential for inexpensive, quick, decentralized testing. Robust analytical sensitivity data in comparison to reverse transcription-quantitative PCR (qRT-PCR) are currently lacking for many rapid antigen tests. Here, we evaluated the analytical sensitivity of the Abbott BinaxNOW COVID-19 Ag card using SARS-CoV-2-positive clinical specimens quantified by reverse transcription-droplet digital PCR (RT-ddPCR) and multiple FDA EUA qRT-PCR platforms using RNA standards. Initial and confirmatory limits of detection for the BinaxNOW COVID-19 Ag card were determined to be equivalent to 4.04 × 10⁴ to 8.06 × 10⁴ copies/swab. We further confirmed this limit of detection with 72 additional clinical samples positive for SARS-CoV-2 in either phosphate-buffered saline or viral transport medium. One hundred percent of samples with viral loads of >40,000 copies/swab were detected by rapid antigen testing. These data indicate that the BinaxNOW COVID-19 Ag card has an analytical sensitivity approximately equivalent to a generic qRT-PCR cycle threshold (C_T) value of 29 to 30.

Rapid electrochemical detection of coronavirus SARS-CoV-2

Coronavirus disease 2019 (COVID-19) is a highly contagious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Diagnosis of COVID-19 depends on quantitative reverse transcription PCR (qRT-PCR), which is time-consuming and requires expensive instrumentation. Here, we report an ultrasensitive electrochemical biosensor based on isothermal rolling circle amplification (RCA) for rapid detection of SARS-CoV-2. The assay involves the hybridization of the RCA amplicons with probes that were functionalized with redox active labels that are detectable by an electrochemical biosensor. The one-step sandwich hybridization assay could detect as low as 1 copy/μL of N and S genes, in less than 2 h. Sensor evaluation with 106 clinical samples, including 41 SARS-CoV-2 positive and 9 samples positive for other respiratory viruses, gave a 100% concordance result with qRT-PCR, with complete correlation between the biosensor current signals and quantitation cycle (Cq) values. In summary, this biosensor could be used as an on-site, real-time diagnostic test for COVID-19.

COVID-19 diagnosis -A review of current methods

A fast and accurate self-testing tool for COVID-19 diagnosis has become a prerequisite to comprehend the exact number of cases worldwide and to take medical and governmental actions accordingly. SARS-CoV-2 (formerly, 2019-nCoV) infection was first reported in Wuhan (China) in December 2019, and then it has rapidly spread around the world, causing ~14 million active cases with ~582,000 deaths as of July 2020. The diagnosis tools available so far have been based on a) viral gene detection, b) human antibody detection, and c) viral antigen detection, among which the viral gene detection by RT-PCR has been found as the most reliable technique. In this report, the current SARS-CoV-2 detection kits, exclusively the ones that were issued an "Emergency Use Authorization" from the U.S. Food and Drug Administration, were discussed. The key structural components of the virus were presented to provide the audience with an understanding of the scientific principles behind the testing tools. The methods that are still in the early research state were also reviewed in a subsection based on the reports available so far.

The prevalence of asymptomatic carriers of COVID-19 as determined by routine preoperative testing

BACKGROUND

The coronavirus disease SARS-CoV-2 (COVID-19) has swiftly spread throughout the globe, greatly influencing all aspects of life. As in previous pandemics, concerns for limited resources and a sustainable medical workforce have been on the forefront of infrastructure modifications. Consequently, surgical specialties have needed to consider each surgical case for necessity and safety during the COVID-19 outbreak. At our institution, availability of SARS-CoV-2 assay has allowed preoperative testing of asymptomatic surgical patients.

AIM/OBJECTIVE

To better define the prevalence of asymptomatic carriers in a surgical population and to better understand the impact of testing on our personal protective equipment (PPE) supply.

METHODS

We began routine, preoperative testing for all asymptomatic patients coming to our academic medical centre on 30 March 2020. Scheduled surgeries were deemed urgent by the surgeon with a review for appropriateness by a novel surgical committee. A retrospective patient chart review was performed. Emergency surgeries were excluded. Asymptomatic patients with positive test results had their surgeries rescheduled at the discretion of the surgeon and patient. Patients who tested negative underwent surgery with staff using standard PPE.

RESULTS

Eighty-four asymptomatic surgical patients were tested preoperatively with three (3.6%) testing positive for SARS-CoV-2. Preoperative testing saved 498 N95 respirators over this time period.

DISCUSSION

This is the first report of routine COVID-19 preoperative testing in an asymptomatic surgical population. Within this population, there is a 3.6% rate of asymptomatic SARS-CoV-2 carriers. Through this practice, personnel exposure can be minimised and access to PPE can be preserved.

Prevalence of SARS-CoV-2 infection in patients presenting for intravitreal injection

Aim

Due to the coronavirus disease 2019 (COVID-19) pandemic, nosocomial transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is of great concern to clinicians of all specialties. Currently there are no published data available on the prevalence of the infection in ophthalmology patients presenting for intravitreal injection (IVI). The purpose of this retrospective study was to estimate the prevalence of SARS-CoV‑2 infection in patients presenting for IVI at our hospital.

Methods

Patients presenting for IVI in April 2020 at our hospital who had been screened for SARS-CoV‑2 infection using nasopharyngeal and oropharyngeal specimen for real-time reverse transcription polymerase chain reaction analysis were included in a retrospective study. To assess the representativity of this sample for IVI patients, characteristics were compared with patients presenting for IVI during March–April 2019.

Results

The study included 279 patients and 319 historic control patients. Of 277 valid test results, one SARS-CoV‑2 positive patient was found, resulting in a carrier rate of 0.36% with a 95% Clopper–Pearson confidence interval of 0.01–1.99%. No differences in sex (57.7% vs. 59.9% female, p = 0.650), age (77.63 ± 10.29 vs. 77.59 ± 10.94 years, p = 0.962), and region of residence were found between groups.

Conclusion

The study provides an estimate for the prevalence of SARS-CoV‑2 infection in asymptomatic patients presenting for IVI. While these data may be used as a baseline, further research is needed to assess the development of SARS-CoV‑2 prevalence in this patient group in order to support risk assessment and infection prevention strategies.

Long-term SARS-CoV-2 RNA shedding and its temporal association to IgG seropositivity

Longitudinal characterization of SARS-CoV-2 PCR testing from COVID-19 patient's nasopharynx and its juxtaposition with blood-based IgG-seroconversion diagnostic assays is critical to understanding SARS-CoV-2 infection durations. Here, we retrospectively analyze 851 SARS-CoV-2-positive patients with at least two positive PCR tests and find that 99 of these patients remain SARS-CoV-2-positive after 4 weeks from their initial diagnosis date. For the 851-patient cohort, the mean lower bound of viral RNA shedding was 17.3 days (SD: 7.8), and the mean upper bound of viral RNA shedding from 668 patients transitioning to confirmed PCR-negative status was 22.7 days (SD: 11.8). Among 104 patients with an IgG test result, 90 patients were seropositive to date, with mean upper bound of time to seropositivity from initial diagnosis being 37.8 days (95% CI: 34.3-41.3). Our findings from juxtaposing IgG and PCR tests thus reveal that some SARS-CoV-2-positive patients are non-hospitalized and seropositive, yet actively shed viral RNA (14 of 90 patients). This study emphasizes the need for monitoring viral loads and neutralizing antibody titers in long-term non-hospitalized shedders as a means of characterizing the SARS-CoV-2 infection lifecycle.

Evaluation of Orthogonal Testing Algorithm for Detection of SARS-CoV-2 IgG Antibodies

BACKGROUND

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody testing is an important tool in assessment of pandemic progress, contact tracing, and identification of recovered coronavirus disease 2019 (COVID-19) patients. We evaluated an orthogonal testing algorithm (OTA) to improve test specificity in these use cases.

METHODS

A two-step OTA was applied where individuals who initially tested positive were tested with a second test. The first-line test, detecting IgG antibodies to the viral nucleocapsid protein, was validated in 130 samples and the second-line test, detecting IgG antibodies to the viral spike protein in 148 samples. The OTA was evaluated in 4333 clinical patient specimens. The seropositivity rates relative to the SARS-CoV-2 PCR positivity rates were evaluated from our entire patient population data (n = 5102).

RESULTS

The first-line test resulted in a clinical sensitivity of 96.4% (95% CI; 82.3% to 99.4%), and specificity of 99.0% (95% CI; 94.7% to 99.8%), whereas the second-line test had a sensitivity of 100% (95% CI; 87.1% to 100%) and specificity of 98.4% (95% CI; 94.2% to 99.5%). Using the OTA, 78/98 (80%) of initially positive SARS-CoV-2 IgG results were confirmed with a second-line test, while 11/42 (26%) of previously diagnosed COVID-19 patients had no detectable antibodies as long as 94 days post PCR diagnosis.

CONCLUSION

Our results show that an OTA can be used to identify patients who require further follow-up due to potential SARS CoV-2 IgG false positive results. In addition, serological testing may not be sufficiently sensitive to reliably detect prior COVID-19 infection.

Cyanoamidine Cyclization Approach to Remdesivir's Nucleobase

We report an alternative approach to the unnatural nucleobase fragment seen in remdesivir (Veklury). Remdesivir displays broad-spectrum antiviral activity and is currently being evaluated in Phase III clinical trials to treat patients with COVID-19. Our route relies on the formation of a cyanoamidine intermediate, which undergoes Lewis acid-mediated cyclization to yield the desired nucleobase. The approach is strategically distinct from prior routes and could further enable the synthesis of remdesivir and other small-molecule therapeutics.

The estimation of diagnostic accuracy of tests for COVID-19: A scoping review

OBJECTIVES

To assess the methodologies used in the estimation of diagnostic accuracy of SARS-CoV-2 real-time reverse transcription polymerase chain reaction (rRT-PCR) and other nucleic acid amplification tests (NAATs) and to evaluate the quality and reliability of the studies employing those methods.

METHODS

We conducted a systematic search of English-language articles published December 31, 2019-June 19, 2020. Studies of any design that performed tests on ≥10 patients and reported or inferred correlative statistics were included. Studies were evaluated using elements of the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) guidelines.

RESULTS

We conducted a narrative and tabular synthesis of studies organized by their reference standard strategy or comparative agreement method, resulting in six categorizations. Critical study details were frequently unreported, including the mechanism for patient/sample selection and researcher blinding to results, which lead to concern for bias.

CONCLUSIONS

Current studies estimating test performance characteristics have imperfect study design and statistical methods for the estimation of test performance characteristics of SARS-CoV-2 tests. The included studies employ heterogeneous methods and overall have an increased risk of bias. Employing standardized guidelines for study designs and statistical methods will improve the process for developing and validating rRT-PCR and NAAT for the diagnosis of COVID-19.

Laboratory diagnosis of severe acute respiratory syndrome coronavirus 2

The first laboratory confirmed case of Coronavirus disease 2019 (COVID-19) in Australia was in Victoria on 25 January 2020 in a man returning from Wuhan city, Hubei province, the People's Republic of China. This was followed by three cases in New South Wales the following day. The Australian Government activated the Australian Health Sector Emergency Response Plan for Novel Coronavirus on 27 February 2020 in anticipation of a pandemic. Subsequently, the World Health Organization declared COVID-19 to be a Public Health Emergency of International Concern followed by a pandemic on 30 January 2020 and 11 March 2020, respectively. Laboratory testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for COVID-19, is key in identifying infected persons to guide timely public health actions of contact tracing and patient isolation to limit transmission of infection. This article aims to provide a comprehensive overview of current laboratory diagnostic methods for SARS-CoV-2, including nucleic acid testing, serology, rapid antigen detection and antibody tests, virus isolation and whole genome sequencing. The relative advantages and disadvantages of the different diagnostic tests are presented, as well as their value in different clinical, infection control and public health contexts. We also describe the challenges in the provision of SARS-CoV-2 diagnostics in Australia, a country with a relatively low COVID-19 incidence in the first pandemic wave but in which prevalence could rapidly change.