Corpus overview


Overview

MeSH Disease

Human Phenotype

Transmission

Seroprevalence
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    Development of mass spectrometry-based targeted assay for direct detection of novel SARS-CoV-2 coronavirus from clinical specimens

    Authors: Santosh Renuse; Patrick M Vanderboom; Anthony D. Maus; Jennifer V. Kemp; Kari M. Gurtner; Anil K. Madugundu; Sandip Chavan; Jane A. Peterson; Benjamin J. Madden; Kiran K. Mangalaparthi; Dong-Gi Mun; Smrita Singh; Benjamin R. Kipp; Surendra Dasari; Ravinder J. Singh; Stefan K. Grebe; Akhilesh Pandey

    doi:10.1101/2020.08.05.20168948 Date: 2020-08-06 Source: medRxiv

    The COVID-19 pandemic caused by severe acute respiratory syndrome MESHD-coronavirus 2 (SARS-CoV-2) has overwhelmed health systems worldwide and highlighted limitations of diagnostic testing. Several types of diagnostics including RT-PCR-based assays, antigen detection by lateral flow assays and antibody SERO-based assays have been developed and deployed in a short time. However, many of these assays are lacking in sensitivity SERO and/or specificity. Here, we describe an immunoaffinity purification followed by high resolution mass spectrometry-based targeted assay capable of detecting viral antigen in nasopharyngeal swab samples of SARS-CoV-2 infected individuals. Based on our discovery experiments using purified virus, recombinant viral protein and nasopharyngeal swab samples from COVID-19 positive patients, nucleocapsid protein was selected as a target antigen. We then developed an automated antibody SERO capture-based workflow coupled to targeted high-field asymmetric ion mobility spectrometry (FAIMS) - parallel reaction monitoring (PRM) assays on an Orbitrap Exploris 480 mass spectrometer. An ensemble machine learning-based model for determining COVID-19 positive samples was created using fragment ion intensities in the PRM data. This resulted in 97.8% sensitivity SERO and 100% specificity with RT-PCR-based molecular testing as the gold standard. Our results demonstrate that direct detection of infectious agents from clinical samples by mass spectrometry-based assays have potential to be deployed as diagnostic assays in clinical laboratories.

    Serology assessment of antibody SERO response to SARS-CoV-2 in patients with COVID-19 by rapid IgM/IgG antibody test SERO

    Authors: Yang De Marinis; Torgny Sunnerhagen; Pradeep Bompada; Anna Blackberg; Runtao Yang; Joel Svensson; Ola Ekstrom; Karl-Fredrik Eriksson; Ola Hansson; Leif Groop; Isabel Goncalves; Magnus Rasmussen

    doi:10.1101/2020.08.05.20168815 Date: 2020-08-06 Source: medRxiv

    The coronavirus disease MESHD 2019 (COVID-19) pandemic has created a global health- and economic crisis. Lifting confinement restriction and resuming to normality depends greatly on COVID-19 immunity screening. Detection of antibodies SERO to severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) which causes COVID-19 by serological methods is important to diagnose a current or resolved infection MESHD. In this study, we applied a rapid COVID-19 IgM/IgG antibody test SERO and performed serology assessment of antibody SERO response to SARS-CoV-2. In PCR-confirmed COVID-19 patients (n=45), the total antibody SERO detection rate is 92% in hospitalized patients and 79% in non-hospitalized patients. We also studied antibody SERO response in relation to time after symptom onset TRANS and disease MESHD severity, and observed an increase in antibody SERO reactivity and distinct distribution patterns of IgM and IgG following disease progression MESHD. The total IgM and IgG detection is 63% in patients with < 2 weeks from disease MESHD onset; 85% in non-hospitalized patients with > 2 weeks disease MESHD duration; and 91% in hospitalized patients with > 2 weeks disease MESHD duration. We also compared different blood SERO sample types and suggest a potentially higher sensitivity SERO by serum SERO/ plasma SERO comparing with whole blood SERO measurement. To study the specificity of the test, we used 69 sera/ plasma SERO samples collected between 2016-2018 prior to the COVID-19 pandemic, and obtained a test specificity of 97%. In summary, our study provides a comprehensive validation of the rapid COVID-19 IgM/IgG serology test, and mapped antibody SERO detection patterns in association with disease MESHD progress and hospitalization. Our study supports that the rapid COVID-19 IgM/IgG test may be applied to assess the COVID-19 status both at the individual and at a population level.

    Swab-Seq: A high-throughput platform for massively scaled up SARS-CoV-2 testing

    Authors: Joshua S. Bloom; Eric M. Jones; Molly Gasperini; Nathan B. Lubock; Laila Sathe; Chetan Munugala; A. Sina Booeshaghi; Oliver F. Brandenberg; Longhua Guo; Scott W. Simpkins; Isabella Lin; Nathan LaPierre; Duke Hong; Yi Zhang; Gabriel Oland; Bianca Judy Choe; Sukantha Chandrasekaran; Evann E. Hilt; Manish J. Butte; Robert Damoiseaux; Aaron R. Cooper; Yi Yin; Lior Pachter; Omai B. Garner; Jonathan Flint; Eleazar Eskin; Chongyuan Luo; Sriram Kosuri; Leonid Kruglyak; Valerie A. Arboleda

    doi:10.1101/2020.08.04.20167874 Date: 2020-08-06 Source: medRxiv

    The rapid spread of severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) is due to the high rates of transmission TRANS by individuals who are asymptomatic TRANS at the time of transmission TRANS. Frequent, widespread testing of the asymptomatic TRANS population for SARS-CoV-2 is essential to suppress viral transmission TRANS and is a key element in safely reopening society. Despite increases in testing capacity, multiple challenges remain in deploying traditional reverse transcription and quantitative PCR (RT-qPCR) tests at the scale required for population screening of asymptomatic TRANS individuals. We have developed SwabSeq, a high-throughput testing platform for SARS-CoV-2 that uses next-generation sequencing as a readout. SwabSeq employs sample-specific molecular barcodes to enable thousands of samples to be combined and simultaneously analyzed for the presence or absence of SARS-CoV-2 in a single run. Importantly, SwabSeq incorporates an in vitro RNA standard that mimics the viral amplicon, but can be distinguished by sequencing. This standard allows for end-point rather than quantitative PCR, improves quantitation, reduces requirements for automation and sample-to-sample normalization, enables purification-free detection, and gives better ability to call true negatives. We show that SwabSeq can test nasal and oral specimens for SARS-CoV-2 with or without RNA extraction while maintaining analytical sensitivity SERO better than or comparable to that of fluorescence-based RT-qPCR tests. SwabSeq is simple, sensitive, flexible, rapidly scalable, inexpensive enough to test widely and frequently, and can provide a turn around time of 12 to 24 hours.

    Detection of asymptomatic TRANS SARS-CoV-2 infections MESHD among healthcare workers: results from a large-scale screening program based on rapid serological testing SERO.

    Authors: Francesca Maria Carozzi; Maria Grazia Cusi; Mauro Pistello; Luisa Galli; Alessandro Bartoloni; Gabriele Anichini; Chiara Azzari; Michele Emdin; Claudia Gandolfo; Fabrizio Maggi; Elisabetta Mantengoli; Maria Moriondo; Giovanna Moscato; Irene Paganini; Claudio Passino; Francesco Profili; Fabio Voller; Marco Zappa; Filippo Quattrone; Gian Maria Rossolini; Paolo Francesconi; - SARS-CoV-2 Serosurvey Tuscan Working Group

    doi:10.1101/2020.07.30.20149567 Date: 2020-08-04 Source: medRxiv

    Abstract Objective: To evaluate the performance SERO of two available rapid immunological tests for identification of severe acute respiratory syndrome MESHD Coronavirus 2 ( SARS-CoV-2) antibodies SERO and their subsequent application to a regional screening of health care workers (HCW) in Tuscany (Italy). Design: measures of accuracy and HCW serological surveillance Setting: 6 major health facilities in Tuscany, Italy. Participants: 17,098 HCW of the Tuscany Region. Measures of accuracy were estimated to assess sensitivity SERO in 176 hospitalized Covid-19 clinical subjects at least 14 days after a diagnostic PCR-positive assay result. Specificity was assessed in 295 sera biobanked in the pre-Covid-19 era in winter or summer 2013-14 Main outcome measures: Sensitivity SERO and specificity, and 95% confidence intervals, were measured using two serological tests SERO, named T-1 and T-2. Positive and Negative predictive values SERO were estimated at different levels of prevalence SERO. HCW of the health centers were tested using the serological SERO tests, with a follow- up nasopharyngeal PCR-test swab in positive tested cases. Results: Sensitivity SERO was estimated as 99% (95%CI: 95%-100%) and 97% (95% CI: 90%-100%), whereas specificity was the 95% and 92%, for Test T-1 and T-2 respectively. In the historical samples IgM cross-reactions were detected in sera collected during the winter period, probably linked to other human coronaviruses. Out of the 17,098 tested, 3.1% have shown the presence of SARS-CoV-2 IgG antibodies SERO, among them 6.8% were positive at PCR follow-up test on nasopharyngeal swabs. Conclusion Based on the low prevalence SERO estimate observed in this survey, the use of serological test SERO as a stand-alone test is not justified to assess the individual immunity status. Serological tests SERO showed good performance SERO and might be useful in an integrated surveillance, for identification of infected subjects and their contacts as required by the policy of contact tracing TRANS, with the aim to reduce the risk of dissemination, especially in health service facilities.

    Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis

    Authors: Rowena A Bull; Thiruni Adikari; Jillian M Hammond; Igor Stevanovski; James M Ferguson; Alicia G Beukers; Zin Naing; Malinna Yeang; Andrey Verich; Hasindu Gamaarachichi; Ki Wook Kim; Fabio Luciani Sr.; Sacha Stelzer-Braid; John-Sebastian Eden; William D Rawlinson; Sebastiaan J van Hal; Ira W Deveson

    doi:10.1101/2020.08.04.236893 Date: 2020-08-04 Source: bioRxiv

    Viral whole-genome sequencing (WGS) provides critical insight into the transmission TRANS and evolution of Severe Acute Respiratory Syndrome MESHD Coronavirus 2 (SARS-CoV-2). Long-read sequencing devices from Oxford Nanopore Technologies (ONT) promise significant improvements in turnaround time, portability and cost, compared to established short-read sequencing platforms for viral WGS (e.g., Illumina). However, adoption of ONT sequencing for SARS-CoV-2 surveillance has been limited due to common concerns around sequencing accuracy. To address this, we performed viral WGS with ONT and Illumina platforms on 157 matched SARS-CoV-2-positive patient specimens and synthetic RNA controls, enabling rigorous evaluation of analytical performance SERO. Despite the elevated error rates observed in ONT sequencing reads, highly accurate consensus-level sequence determination was achieved, with single nucleotide variants (SNVs) detected at >99% sensitivity SERO and >98% precision above a minimum ~60-fold coverage depth, thereby ensuring suitability for SARS-CoV-2 genome analysis. ONT sequencing also identified a surprising diversity of structural variation within SARS-CoV-2 specimens that were supported by evidence from short-read sequencing on matched samples. However, ONT sequencing failed to accurately detect short indels and variants at low read-count frequencies. This systematic evaluation of analytical performance SERO for SARS-CoV-2 WGS will facilitate widespread adoption of ONT sequencing within local, national and international COVID-19 public health initiatives.

    Assessment of a Laboratory-Based SARS-CoV-2 Antibody SERO Test Among Hemodialysis Patients: A Quality Improvement Initiative

    Authors: Dena E Cohen; Gilbert Marlowe; Gabriel Contreras; Marie Ann Sosa; Jair Munoz Mendoza; Oliver Lenz; Zain Mithani; Pura Margarita Teixeiro; Nery Queija; Araceli Moneda; Jean S Jeanty; Katherine Swanzy; Misha Palecek; Mahesh Krishnan; Jeffery Giullian; Steven M Brunelli

    doi:10.1101/2020.08.03.20163642 Date: 2020-08-04 Source: medRxiv

    Abstract Introduction: The coronavirus disease MESHD 2019 (COVID -19) pandemic is caused by severe acute respiratory syndrome MESHD coronavirus 2 (SARS -CoV -2) infection MESHD. Although tests to detect anti - SARS -CoV-2 antibodies SERO have been developed, their sensitivity SERO and specificity in hemodialysis patients have not been previously assessed. Methods: As part of a quality improvement (QI) initiative, nasopharyngeal swabs and predialysis blood SERO samples were collected on the same day from adult TRANS patients receiving routine hemodialysis care at clinics managed by a large dialysis organization in the greater Miami, Florida region (23 - 30 Apr 2020). Polymerase chain reaction (PCR) tests for SARS -CoV -2 and chemiluminescence immunoassays SERO for anti -SARS -CoV2 antibodies SERO were performed according to manufacturer-specified protocols. Results: Of 715 participants in the QI initiative, 38 had symptomatology consistent with COVID -19 prior to or during the initiative. Among these, COVID -19 was PCR -confirmed in 14 and ruled out in 20, with the remaining 4 being inconclusive. Among the 34 patients with known COVID -19 status, the sensitivity SERO and specificity of the antibody test SERO were 57.1% and 85.0% when either antibody SERO was considered. The remaining 677 patients had no record of symptoms consistent with COVID -19, nor any known exposure. Of these, 38 patients (5.6%) tested positive for anti- SARS-CoV-2 antibodies SERO. Conclusions: The operational characteristics of the laboratory-based antibody test SERO make it sufficient to rule in, but not rule out, SARS -CoV -2 infection MESHD in the appropriate clinical circumstance. A substantial proportion of dialysis patients may have had asymptomatic TRANS SARS -CoV -2 infection MESHD.

    Clinical Utility of a Highly Sensitive Lateral Flow Immunoassay SERO as determined by Titer Analysis for the Detection of anti- SARS-CoV-2 Antibodies SERO at the Point-of-Care

    Authors: Amanda Haymond; Claudius Mueller; Hannah Steinberg; K. Alex Hodge; Caitlin W Lehman; Shih-Chao Lin; Lucia Collini; Heather Branscome; Tuong Vi Nguyen; Sally Rucker; Lauren Panny; Rafaela Flor; Raouf Guirguis; Richard Hoefer; Giovanni Lorenzin; Emanuel Petricoin; Fatah Kashanchi; Kylene Kehn-Hall; Paolo Lanzafame; Lance Liotta; Alessandra Luchini

    doi:10.1101/2020.07.30.20163824 Date: 2020-08-02 Source: medRxiv

    Coronavirus disease MESHD 2019 (COVID-19), caused by the severe acute respiratory syndrome MESHD coronavirus-2 (SARS-CoV-2), became a pandemic in early 2020. Lateral flow immunoassays SERO for antibody testing SERO have been viewed as a cheap and rapidly deployable method for determining previous infection MESHD with SARS-CoV-2; however, these assays have shown unacceptably low sensitivity SERO. We report on nine lateral flow immunoassays SERO currently available and compare their titer sensitivity SERO in serum SERO to a best-practice enzyme-linked immunosorbent assay SERO ( ELISA SERO) and viral neutralization assay. For a small group of PCR-positive, we found two lateral flow immunoassay SERO devices with titer sensitivity SERO roughly equal to the ELISA SERO; these devices were positive for all PCR-positive patients harboring SARS-CoV-2 neutralizing antibodies SERO. One of these devices was deployed in Northern Italy to test its sensitivity SERO and specificity in a real-world clinical setting. Using the device with fingerstick blood SERO on a cohort of 27 hospitalized PCR-positive patients and seven hospitalized controls, ROC curve analysis gave AUC values of 0.7646 for IgG. For comparison, this assay was also tested with saliva from the same patient population and showed reduced discrimination between cases and controls with AUC values of 0.6841 for IgG. Furthermore, during viral neutralization testing, one patient was discovered to harbor autoantibodies to ACE2, with implications for how immune responses are profiled. We show here through a proof-of-concept study that these lateral flow devices can be as analytically sensitive as ELISAs SERO and adopted into hospital protocols; however, additional improvements to these devices remain necessary before their clinical deployment.

    Persistence of anti- SARS-CoV-2 antibodies SERO in non-hospitalized COVID-19 convalescent health care workers

    Authors: Margherita Bruni; Valentina Cecatiello; Angelica Diaz-Basabe; Georgia Lattanzi; Erika Mileti; Silvia Monzani; Laura Pirovano; Francesca Rizzelli; Clara Visintin; Giuseppina Bonizzi; Marco Giani; Marialuisa Lavitrano; Silvia Faravelli; Federico Forneris; Flavio Caprioli; Pier Giuseppe Pelicci; Gioacchino Natoli; Sebastiano Pasqualato; Marina Mapelli; Federica Facciotti

    doi:10.1101/2020.07.30.20164368 Date: 2020-08-01 Source: medRxiv

    Background. Coronavirus disease MESHD-19 (COVID-19) is a respiratory illness caused by the Severe Acute Respiratory Syndrome MESHD CoronaVirus 2 (SARS-CoV-2), a novel beta-coronavirus. Although antibody SERO response to SARS-CoV-2 can be detected early during the infection MESHD, several outstanding questions remain to be addressed regarding magnitude and persistence of antibody SERO titer against different viral proteins and their correlation with the strength of the immune response, as measured by serum SERO levels of pro-inflammatory mediators. Methods. An ELISA assay SERO has been developed by expressing and purifying the recombinant SARS-CoV-2 Spike Receptor Binding Domain (RBD), Soluble Ectodomain (Spike), and full length nucleocapsid protein (N protein). Sera from healthcare workers affected by non-severe COVID-19 were longitudinally collected over four weeks, and compared to sera from patients hospitalized in Intensive Care Units (ICU) and SARS-CoV-2-negative subjects for the presence of IgM, IgG and IgA antibodies SERO as well as soluble pro-inflammatory mediators in the sera. Results. Specificity and sensitivity SERO of the ELISA assays SERO were high for anti-RBD IgG and IgA (92-97%) and slightly lower for IgM and the Spike and N proteins (70-85%). The ELISA SERO allowed quantification of IgM, IgG and IgA antibody SERO responses against all the viral antigens tested and showed a correlation between magnitude of the antibody SERO response and disease MESHD severity. Non-hospitalized subjects showed lower antibody SERO titers and blood SERO pro-inflammatory cytokine profiles as compared to patients in Intensive Care Units (ICU), irrespective of the antibodies tested SERO. Noteworthy, in non-severe COVID-19 infections MESHD, antibody SERO titers against RBD and Spike, but not against the N protein, as well as pro-inflammatory cytokines decreased within a month after viral clearance. Conclusions. Rapid decline in antibody SERO titers and in pro-inflammatory cytokines may be a common feature of non-severe SARS-CoV-2 infection MESHD, suggesting that antibody SERO-mediated protection against re- infection MESHD with SARS-CoV-2 is of short duration. These results suggest caution in use serological testing SERO to estimate the prevalence SERO of SARS-CoV-2 infection MESHD in the general population.

    Fighting COVID-19 spread among nursing home residents even in absence of molecular diagnosis: a retrospective cohort study.

    Authors: Alessio Strazzulla; Paul Tarteret; Maria Concetta Postorino; Marie Picque; Astrid de Pontfarcy; Nicolas Vignier; Catherine Chakvetadze; Coralie Noel; Cecile Drouin; Zine Eddine Benguerdi; Sylvain Diamantis

    doi:10.21203/rs.3.rs-51305/v1 Date: 2020-07-30 Source: ResearchSquare

    Background Access to molecular diagnosis was limited out-of-hospital in France during the 2020 coronavirus disease MESHD 2019 (COVID-19) epidemic. This study describes the evolution of COVID-19 outbreak in a nursing home in absence of molecular diagnosis. Methods A monocentric prospective study was conducted in a French nursing home from March 17th, 2020 to June 11th, 2020. Because of lack of molecular tests for severe acute respiratory syndrome MESHD 2 (SARS-Cov2) infection MESHD, probable COVID-19 cases were early identified considering only respiratory and not-respiratory symptoms and therefore preventing measures and treatments were enforced. Once available, serology tests were performed at the end of the study.A chronologic description of new cases and deaths MESHD was made together with a description of COVID-19 symptoms. Data about personal characteristics and treatments were collected and the following comparisons were performed: i) probable COVID-19 cases vs asymptomatic TRANS residents; ii) SARS-Cov2 seropositive residents vs seronegative residents. Results Overall, 32/66 (48.5%) residents and 19/39 (48.7%) members of health-care personnel were classified as probable COVID-19 cases. A total of 34/61 (55.7%) tested residents resulted seropositive. Death MESHD occurred in 4/66 (6%) residents. Diagnosis according to symptoms had 65% of sensitivity SERO, 78% of specificity, 79% of positive predictive value SERO and 64% of negative predictive value SERO.In resident population, the following symptoms were registered: 15/32 (46.8%) lymphopenia MESHD lymphopenia HP, 15/32 (46.8%) fever MESHD fever HP, 8/32 (25%) fatigue MESHD fatigue HP, 8/32 (25%) cough MESHD cough HP, 6/32 (18.8%) diarrhoea, 4/32 (12.5%) severe respiratory distress HP requiring oxygen therapy, 4/32 (12.5%) fall HP, 3/32 (9.4%) conjunctivitis MESHD conjunctivitis HP, 2/32 (6.3%) abnormal pulmonary noise at chest examination and 2/32 (6,25%) abdominal pain MESHD abdominal pain HP. Probable COVID-19 cases were older (81.3 vs 74.9; p=0.007) and they had higher prevalence SERO of atrial fibrillation MESHD atrial fibrillation HP (8/32, 25% vs 2/34, 12%; p=0.030); insulin treatment (4/34, 12% vs 0, 0%; p=0.033) and positive SARS-Cov2 serology (22/32, 69% vs 12/34, 35%; p=0.001) than asymptomatic TRANS residents. Seropositive residents had lower prevalence SERO of diabetes (4/34, 12% vs 9/27, 33%; p=0.041) and angiotensin-converting-enzyme inhibitors’ intake (1/34, 1% vs 5/27, 19%; p=0.042). Conclusions During SARS-Cov2 epidemic, early detection of respiratory and not-respiratory symptoms allowed to enforce extraordinary measures. They achieved limiting contagion and deaths MESHD among nursing home residents, even in absence of molecular diagnosis.

    A Non-Adaptive Combinatorial Group Testing Strategy to Facilitate Healthcare Worker Screening During the Severe Acute Respiratory Syndrome MESHD Coronavirus-2 (SARS-CoV-2) Outbreak

    Authors: John Henry McDermott; Duncan Stoddard; Peter Woolf; Jamie M Ellingford; David Gokhale; Algy Taylor; Leigh AM Demain; William G Newman; Graeme Black

    doi:10.1101/2020.07.21.20157677 Date: 2020-07-30 Source: medRxiv

    Background: Regular SARS-CoV-2 testing of healthcare workers (HCWs) has been proposed to prevent healthcare facilities becoming persistent reservoirs of infectivity. Using monoplex testing, widespread screening would be prohibitively expensive, and throughput may not meet demand. We propose a non-adaptive combinatorial (NAC) group-testing strategy to increase throughput and facilitate rapid turnaround via a single round of testing. Methods: NAC matrices were constructed for sample sizes of 700, 350 and 250 with replicates of 2, 4 and 5, respectively. Matrix performance SERO was tested by simulation under different SARS-CoV-2 prevalence SERO scenarios of 0.1-10%, with each simulation ran for 10,000 iterations. Outcomes included the proportions of re-tests required and the proportion of true negatives identified. NAC matrices were compared to Dorfman Sequential (DS) approaches. A web application (www.samplepooling.com) was designed to decode results. Findings: NAC matrices performed well at low prevalence SERO levels with an average number of 585 tests saved per assay in the n=700 matrix at a 1% prevalence SERO. As prevalence SERO increased, matrix performance SERO deteriorated with n=250 most tolerant. In simulations of low to medium (0.1%-3%) prevalence SERO levels all NAC matrices were superior, as measured by fewer repeated tests required, to the DS approaches. At very high prevalence SERO levels (10%) the DS matrix was marginally superior, however both group testing approaches performed poorly at high prevalence SERO levels. Interpretation: This testing strategy maximises the proportion of samples resolved after a single round of testing, allowing prompt return of results to staff members. Using the methodology described here, laboratories can adapt their testing scheme based on required throughput and the current population prevalence SERO, facilitating a data-driven testing strategy.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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