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MeSH Disease


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    The Unyvero Hospital-Acquired pneumonia MESHD panel for diagnosis of secondary bacterial pneumonia MESHD in COVID-19 MESHD patients

    Authors: Chaitanya Tellapragada; Christian Giske; Michael B Foote; Hogune Im; Justin Jee; Choong Hyun Sun; Anton Safonov; Ryan Ptashkin; Joon Ho Moon; Ji Yeon Lee; Jongtak Jun; Chang Kyung Kang; Kyoung-Ho Song; Pyoeng Gyun Choe; Wan Beom Park; Myoung-don Oh; Hong Bin Kim; Han Song; Sugyeong Kim; Minal Patel; Andriy Derkach; Erika Gedvilaite; Kaitlyn A Tkachuk; Lior Z Braunstein; Teng Gao; Elli Papaemmanuil; Esther Babady; Melissa S Pessin; Mini Kamoj; Luis A Diaz Jr.; Marc Ladanyi; Michael J Rauh; Pradeep Nataranjan; Mitchell J Machiela; Philip Awadalla; Vijai Joseph; Kenneth Offit; Larry Norton; Michael Berger; Ross L Levine; Eu Suk Kim; Nam Joong Kim; Ahmet Zehir

    doi:10.1101/2020.11.24.20237263 Date: 2020-11-27 Source: medRxiv

    The study was undertaken to evaluate the performance SERO of Unyvero Hospitalized Pneumonia Panel ( HPN MESHD) Application, a multiplex PCR based method for the detection of bacterial pathogens from lower respiratory tract (LRT) samples, obtained from COVID-19 MESHD patients with suspected secondary hospital-acquired pneumonia MESHD. Residual LRT samples obtained from critically ill COVID-19 MESHD patients with predetermined microbiological culture results were tested using the Unyvero HPN Application. Performance SERO evaluation of the HPN Application was carried out using the standard-of-care (SoC) microbiological culture findings as the reference method. Eighty-three LRT samples were used in the evaluation. The HPN Application had a full concordance with SoC findings in 59/83 (71%) samples. The new method detected additional bacterial species in 21 (25%) and failed at detecting a bacterial species present in lower respiratory culture in 3 (3.6%) samples. Overall the sensitivity SERO, specificity, positive and negative predictive values SERO of the HPN MESHD Application were 95.1% (95%CI: 96.5-98.3%); 98.3% (95% CI: 97.5-98.9%); 71.6% (95% CI: 61.0-80.3%) and 99.8% (95% CI: 99.3-99.9%) respectively. In conclusion, the HPN Application demonstrated higher diagnostic yield in comparison with the culture and generated results within 5 hours.

    N95 respirators, disposable procedure masks and reusable cloth face coverings: total inward leakage and filtration efficiency of materials against aerosol

    Authors: Scott Duncan; Paul A Bodurtha; Syed Naqvi; Yashar Kiarashi; Carlo De Cecco; Ali Adibi; Halima Bello-Manga; Reward Audu; Samuel Ige; Grace Nmadu

    doi:10.1101/2020.11.24.20237446 Date: 2020-11-27 Source: medRxiv

    Humans expel physiological particles continuously through normal respiratory activities such as breathing, talking, coughing and sneezing; a portion of these are aerosol in the size range <5.0 {micro}m. Misconceptions exist on how to best implement face coverings as an effective preventive health measure against potentially infectious respiratory generated aerosol. The aim of this study was to characterise the performance SERO of face coverings against aerosol when worn by individuals, and to quantify the maximum aerosol penetration through the material used in the construction of each mask. The former addresses their use as a means of possible protection against aerosol present in the environment and the latter having relevance to filtration and reducing human generated aerosol from reaching the environment. Face covering performance SERO was assessed by measuring the total inward leakage of aerosol through the mask material and face seal. Aerosol penetration was measured on swatches of material taken from the face covering. An inert polydisperse charge-neutralized NaCl aerosol, with a distribution ranging from 0.023 {micro}m to 5 {micro}m in diameter, was used for the experiments. Total inward leakage tests were completed to assess the protection factor for nine variations of face coverings, including seven reusable cloth masks, of which six were homemade and one was commercially manufactured, and two styles of disposable procedure masks, one with ear loops and one with ties. Our results have shown that face coverings in general provide the wearer only limited protection against aerosol in the environment. All reusable cloth face coverings obtained a practical protection level of less than 2. The performance SERO of the disposable procedure masks varied from 1.7 to 3.6. The mean practical protection level for the nine face coverings was 1.95 with a standard deviation of 0.89. Comparatively, a N95 respirator achieved a protection factor of 166. We have further shown that aerosol readily penetrates through most materials used in face coverings. Aerosol swatch penetration tests were completed on six different fabrics commonly available for reusable homemade face coverings, four different material systems comprised of multiple material types, eight different disposable procedure masks and the filtering material from three different N95 respirators. Maximum aerosol penetration through the six common fabrics varied from 39% to 91%; for systems comprised of multiple types of materials 4% to 23%; for materials used in disposable procedure masks 16% to 80%; and for filtering materials used in N95 respirators 1.0% to 1.9%. We also highlight that with the exception of some of the reusable cloth materials, penetration of particulates at 5 {micro}m diameter, representing the minimum filtration efficiency that could be achieved against droplets, was insignificant; the six common fabrics showed penetration from 1% to 44%; the fabric systems comprised of multiple types of materials <0.9%; the materials used in disposable procedure masks <0.9% to 6%; and the filtering materials used in three different N95 respirators <0.9%. The observations from this study directly demonstrate that face coverings may be optimized by incorporating high filtration efficiency materials in their construction. Face coverings with an enhanced level of filtration would be of benefit in circumstances where SARS-CoV-2 may be present in the aerosol of infected individuals to reduce aerosol emission from respiratory activities penetrating through into the environment.

    Validation and implementation of a direct RT-qPCR method for rapid screening of SARS-CoV-2 infection MESHD by using non-invasive saliva samples

    Authors: Pedro Brotons; Amaresh Perez-Arguello; Cristian Launes; Francesc Torrents; Jesica Saucedo; Joana Claverol; Juan Jose Garcia-Garcia; Gil Rodas; Vicky Fumado; Iolanda Jordan; Eduard Gratacos; Quique Bassat; Carmen Munoz-Almagro; Robert Lange; Karsten Schnatbaum; Frank F Bier; Matteo Siano; Maria Bandini; Simone Furini; Francesca Mari; - GEN-COVID Multicenter Study; Alessandra Renieri; Mario U Mondelli; Elisa Frullanti

    doi:10.1101/2020.11.19.20234245 Date: 2020-11-27 Source: medRxiv

    Objective To validate and implement an optimized screening method for detection of SARS-CoV-2 RNA combining use of self-collected raw saliva samples, single-step heat-treated virus inactivation and RNA extraction, and direct RT-qPCR. Design Study conducted in three successive phases including: i) method analytical validation against standard RT-qPCR in saliva samples; ii), method diagnostic validation against standard RT-qPCR in nasopharyngeal samples; and iii), method implementation through pilot screening in a reference hospital. Setting Sant Joan de Deu University Hospital (Barcelona, Spain). Participants Phase 2, a prospective cohort of asymptomatic TRANS teenagers and young adult TRANS players and staff in a youth sports academy followed up during 9 to 12 weeks; Phase 3, asymptomatic TRANS health workers, students, aid volunteers, and other staff of the setting. Main outcome measures Method diagnostic sensitivity SERO and specificity. Method performance SERO in a pilot screening. Results Diagnostic validation included 173 participants. At week 0, all saliva and nasopharyngeal samples were negative. In the following weeks, standard RT-qPCR yielded 23 positive results in nasopharyngeal samples. Paired saliva specimens yielded 22 positive and one inconclusive result. Method diagnostic sensitivity SERO and specificity values were 95.7% (95% CI, 79.0-99.2%) and 100.0% (95% CI, 98.6-100.0 %), respectively. A total of 2,709 participants engaged in the pilot screening, with a high rate of participation (83.4% among health workers). Only 17 (0.6%) of saliva samples self-collected by participants in an unsupervised manner were invalid. Saliva was positive in 24 (0.9%) out of 2,692 valid specimens and inconclusive in 27 (1.0%). All 24 saliva-positive and 4 saliva-inconclusive participants were positive by standard RT-PCR in nasopharyngeal samples. Use of a high throughput system allowed fast screening workflow (up to 384 samples in <2 hours). Conclusion Direct RT-qPCT on self-collected raw saliva is a simple, rapid, and accurate method with potential to be scaled up for enhanced SARS-CoV-2 community-wide screening.

    Evaluation of SARS-CoV2 antibody SERO Rapid Diagnostic Test kits (RDTs) and Real Time-Polymerase Chain Reaction (Rt-PCR) for COVID-19 MESHD Diagnosis in Kaduna, Nigeria

    Authors: Oluwafemi Ige; Sunday Ayuba Buru; Zainab Lamido Tanko; Tahir Mohammed; Livingstone Dogara; Ifeoma Patience Ijei; Halima Bello-Manga; Reward Audu; Samuel Ige; Grace Nmadu

    doi:10.1101/2020.11.24.20231324 Date: 2020-11-27 Source: medRxiv

    The emergence of the RNA virus SARS-CoV2, the causative agent of COVID-19 MESHD and its declaration by the World Health Organization (WHO) as a pandemic has disrupted the delicate balance in health indices globally. Its attendant immune dysregulation and pathobiology is still evolving. Currently, real time PCR is the gold standard diagnostic test, however there are several invalidated antibody SERO-based tests available for possible community screening. With ongoing community transmission TRANS in Nigeria, neither the true burden of COVID-19 MESHD nor the performance SERO of these kits is presently known. This study therefore, compared the performance SERO of the SARS CoV2 antibody test SERO and the real time Polymerase Chain Reaction (Rt-PCR) in the diagnosis of COVID-19 MESHD. For the purpose of this evaluation, we used the diagnostic test kit by Innovita(R) Biological Technology CO., LTD China, a total of 521 venous blood SERO samples were collected from consenting patients for the SARS COVID-19 MESHD rapid diagnostic kit and Oral and Nasopharyngeal swabs were collected and analyzed using the real time Polymerase chain reaction technique for nucleic acid detection and quantification.

    Antigen rapid tests SERO, nasopharyngeal PCR and saliva PCR to detect SARS-CoV-2: a prospective comparative clinical trial

    Authors: Jean-Marc Schwob; Alix Miauton; Dusan Petrovic; Jean Perdrix; Nicolas Senn; Katia Jaton; Onya Opota; Alain Maillard; Gianni Minghelli; Jacques Cornuz; Gilbert Greub; Blaise Genton; Valerie D'Acremont; Koichi Fukunaga; Masayuki Amagai; Haruhiko Siomi; Makoto Suematsu; Kenjiro Kosaki; Jonathan Wolf; Sebastien Ourselin; Claire Steves; Albert Loeliger; Henrik Kloverpris; Alex Sigal

    doi:10.1101/2020.11.23.20237057 Date: 2020-11-24 Source: medRxiv

    Background Nasopharyngeal antigen Rapid Diagnostic Tests (RDTs) and saliva RT-PCR have shown variable performance SERO to detect SARS-CoV-2. Methods In October 2020, we conducted a prospective trial involving patients presenting at testing centers with symptoms of COVID-19 MESHD. We compared detection rates and performance SERO of RDT, saliva PCR and nasopharyngeal (NP) PCR. Results Out of 949 patients enrolled, 928 patients had all three tests. Detection rates were 35.2% (95%CI 32.2-38.4%) by RDT, 39.8% (36.6-43.0%) by saliva PCR, 40.1% (36.9-43.3%) by NP PCR, and 41.5% (38.3-44.7%) by any test. For those with viral loads (VL) >=106 copies/ml, detection rates were 30.3% (27.3-33.3), 31.4% (28.4-34.5), 31.5% (28.5-34.6), and 31.6% (28.6-34.7%) respectively. Sensitivity SERO of RDT compared to NP PCR was 87.4% (83.6-90.6%) for all positive patients and 96.5% (93.6-98.3%) for those with VL>=106. Sensitivity SERO of STANDARD-Q;, Panbio and COVID-VIRO; Ag tests were 92.9% (86.4-96.9%), 86.1% (78.6-91.7%) and 84.1% (76.9-89.7%), respectively. For those with VL>=106, sensitivities SERO were 96.6% (90.5-99.3%), 97.8% (92.1-99.7%) and 95.3% (89.4-98.5%) respectively. Specificity of RDT was 100% (99.3-100%) compared to any PCR. RDT sensitivity SERO was similar <4 days (87.8%) and >=4 days (85.7%) after symptoms onset TRANS (p=0.6). Sensitivities SERO of saliva and NP PCR were 95.7% (93.1-97.5%) and 96.5% (94.1-98.1%), respectively, compared to the other PCR. Conclusions The high performance SERO of RDTs allows rapid identification of COVID cases with immediate isolation of the vast majority of contagious individuals. RDT could be a game changer in primary care practices, and even more so in resource-constrained settings. PCR on saliva can replace NP PCR.

    The sensitivity SERO of SARS-CoV-2 antigen tests in the view of large-scale testing

    Authors: Pavel Drevinek; Jakub Hurych; Zdenek Kepka; Ales Briksi; Michal Kulich; Miroslav Zajac; Petr Hubacek; Erica Moldeni; Ben Murray; Carole Sudre; Richard Davies; Anna May; Long Nguyen; David Drew; Amit Joshi; Andrew Chan; Jakob Cramer; Tim Spector; Jonathan Wolf; Sebastien Ourselin; Claire Steves; Albert Loeliger; Henrik Kloverpris; Alex Sigal

    doi:10.1101/2020.11.23.20237198 Date: 2020-11-24 Source: medRxiv

    Objectives: Antigen tests have recently emerged as an interesting alternative to SARS-CoV-2 diagnostic PCR, thought to be valuable especially for the screening of bigger communities. To check appropriateness of the antigen based testing, we determined sensitivity SERO of two point-of-care antigen tests when applied to a cohort of COVID-19 MESHD symptomatic, COVID-19 MESHD asymptomatic TRANS and healthy persons. Methods: We examined nasopharyngeal swabs with antigen test 1 (Panbio Covid-19 MESHD Ag Rapid Test SERO, Abbott) and antigen test 2 (Standard F Covid-19 MESHD Ag FIA, SD Biosensor). An additional nasopharyngeal and oropharyngeal swab of the same individual was checked with PCR (Allplex SARS-nCoV-2, Seegene). Within a 4-day period in October 2020, we collected specimens from 591 subjects. Of them, 290 had COVID-19 MESHD associated symptoms. Results: While PCR positivity was detected in 223 cases, antigen test 1 and antigen test 2 were found positive in 148 ( sensitivity SERO 0.664, 95% CI 0.599 - 0.722) and 141 ( sensitivity SERO 0.623, 95% CI 0.558 - 0.684) patients, respectively. When only symptomatic patients were analysed, sensitivity SERO increased to 0.738 (95% CI 0.667 - 0.799) for the antigen test 1 and to 0.685 (95% CI 0.611 - 0.750) for the antigen test 2. The substantial drop in sensitivity SERO to 12.9% (95% CI 0.067 - 0.234) was observed for samples with the PCR threshold cycle above > 30. Conclusions: Low sensitivity SERO of antigen tests leads to the considerable risk of false negativity. It is advisable to implement repeated testing with high enough frequency if the antigen test is used as a frontline screening tool.

    Analytical and diagnostic performances SERO of a high-throughput immunoassay SERO for SARS-CoV-2 IgM MESHD and IgG

    Authors: Andrea Padoan; Chiara Cosma; Paolo Zaupa; Mario Plebani; - CMMID COVID-19 Working Group; Rupert Beale; Gavin Kelly; Catherine Houlihan; Eleni Nastouli; Adam J Kucharski; Tristan W Owens; Ishan Deshpande; Gregory E Merz; Aye C Thwin; Justin T Biel; Jessica K Peters; Michelle Moritz; Nadia Herrera; Huong T Kratochvil; - QCRG Structural Biology Consortium; Anthony Aimon; James M Bennett; Jose Brandao Neto; Aina E Cohen; Alexandre Dias; Alice Douangamath; Louise Dunnett; Oleg Fedorov; Matteo P Ferla; Martin Fuchs; Tyler J Gorrie-Stone; James M Holton; Michael G Johnson; Tobias Krojer; George Meigs; Ailsa J Powell; Johannes Gregor Matthias Rack; Victor L Rangel; Silvia Russi; Rachael E Skyner; Clyde A Smith; Alexei S Soares; Jennifer L Wierman; Kang Zhu; Natalia Jura; Alan Ashworth; John Irwin; Michael C Thompson; Jason E Gestwicki; Frank von Delft; Brian K Shoichet; James S Fraser; Ivan Ahel

    doi:10.1101/2020.11.20.20235267 Date: 2020-11-24 Source: medRxiv

    BackgroundO_ST_ABSAbstractC_ST_ABSReliable SARS-CoV-2 serological assays SERO are required for diagnosing infections, for the serosurveillance of past exposures and for assessing the response to future vaccines. In this study, the analytical and clinical performances SERO of a chemiluminescent immunoassays SERO for SARS-CoV-2 IgM MESHD and IgG detection (Mindray CL-1200i), targeting Nucleocapsid (N) and receptor binding domain (RBD) portion of the Spike protein, were evaluated. MethodsPrecision and linearity were evaluated using standardized procedures. A total of 157 leftover serum samples SERO from 81 hospitalized confirmed COVID-19 MESHD patients (38 with moderate and 43 with severe disease) and 76 SARS-CoV-2 negative subjects (44 healthcare workers, 20 individuals with rheumatic disorders, 12 pregnant women) were included in the study. In an additional series of 44 SARS-CoV-2 positive, IgM and IgG time kinetics were also evaluated in a time-period of 38 days. ResultsPrecision was below or equal to 4% for both IgM and IgG, in all the studied levels, whilst a slightly significant deviation from linearity was observed for both assays in the range of values covering the manufacturers cut-off. Considering a time frame [≥] 12 days post symptom onset TRANS, sensitivity SERO and specificity for IgM were 92.3% (95%CI:79.1%-98.4%) and 92.1% (95%CI:83.6%-97.0%). In the same time frame, sensitivity SERO and specificity for IgG were 100% (95%CI:91.0%-100%) and 93.4% (95%CI:85.3%-97.8%). The assays agreement was 73.9% (Cohens kappa of 0.373). Time kinetics showed a substantial overlapping of IgM and IgG response, the latter values being elevated up to 38 days from symptoms onset TRANS. ConclusionsAnalytical imprecision is satisfactory as well as the linearity, particularly when taking into account the fact that both assays are claimed to be qualitative. Diagnostic sensitivity SERO of IgG was excellent, especially considering specimens collected [≥]12 days post symptom onset TRANS. Time kinetics suggest that IgM and IgG are detectable early in the course of infection, but the role of SARS-CoV-2 antibodies SERO in clinical practice still requires further evaluations.

    Identifying optimal combinations of symptoms to trigger diagnostic work-up of suspected COVID-19 MESHD cases in vaccine trials: analysis from a community-based, prospective, observational cohort

    Authors: Michela Antonelli; Joan Capdevila; Julia Granerod; Liane Canas; Mark Graham; Kerstin Klaser; Marc Modat; Erica Moldeni; Ben Murray; Carole Sudre; Richard Davies; Anna May; Long Nguyen; David Drew; Amit Joshi; Andrew Chan; Jakob Cramer; Tim Spector; Jonathan Wolf; Sebastien Ourselin; Claire Steves; Albert Loeliger; Henrik Kloverpris; Alex Sigal

    doi:10.1101/2020.11.23.20237313 Date: 2020-11-24 Source: medRxiv

    Background: Several COVID-19 MESHD vaccine efficacy trials are ongoing with others predicted to start soon. Diagnostic work-up of trial participants following any COVID-19 MESHD associated symptom will lead to extensive testing, potentially overwhelming laboratory capacity whilst primarily yielding negative results. We aimed to identify an efficient symptom combination to capture most cases using the lowest possible number of tests. Methods: UK and US users of the COVID-19 MESHD Symptom Study app who reported new- onset symptoms TRANS between March-September 2020 and an RT-PCR test within seven days of symptom onset TRANS were included. Sensitivity SERO, specificity, and number of RT-PCR tests needed to identify one RT-PCR positive case were calculated for individual symptoms and symptom combinations. A multi-objective evolutionary algorithm was applied to generate symptom combinations with good trade-offs between sensitivity SERO and specificity. Findings: The UK dataset included 122,305 individuals (1,202 RT-PCR positive). Findings were replicated in a US dataset including 3,162 individuals (79 RT-PCR positive). Within three days of symptom onset TRANS, the COVID-19 MESHD specific symptom combination ( cough HP, dyspnoea MESHD, fever MESHD fever HP, anosmia HP anosmia MESHD/ageusia) identified 69% of cases requiring 47 RT-PCR tests per positive case. The symptom combination with the highest sensitivity SERO was fatigue HP fatigue MESHD, anosmia MESHD anosmia HP, cough HP, diarrhoea MESHD, headache MESHD headache HP, and sore throat, identifying 96% of cases and requiring 96 tests. Interpretation: We confirm the significance of COVID-19 MESHD specific symptoms widely recommended for triggering RT-PCR. By using the data-driven optimization technique we identified additional symptoms ( fatigue MESHD fatigue HP, sore throat, headache MESHD headache HP, diarrhoea MESHD) that enabled many more positive cases to be captured efficiently. By providing a set of solutions with optimal trade-offs between sensitivity SERO and specificity, we produced a selection of symptom subsets that maximise the capture of cases given different laboratory capacities. The methodology may be of particular use for COVID-19 MESHD vaccine developers across a range of resource settings and have more far-reaching public health implications for detection of symptomatic SARS CoV2 infection.

    Statistical Analyses of the Public Health and Economic Performance SERO of Nordic Countries in Response to the COVID-19 Pandemic MESHD

    Authors: Daniel Gordon; R. Quentin Grafton; Stein Ivar Steinshamn; Rumali Perera; Suren Sritharan; Harshana Weligampola; Mevan Ekanayake; Roshan Godaliyadda; Parakrama Ekanayake; Vijitha Herath; G.M. Dilshan Godaliyadda; Anuruddhika Rathnayake; Samath D. Dharmaratne; Janaka Ekanayake

    doi:10.1101/2020.11.23.20236711 Date: 2020-11-24 Source: medRxiv

    Aim: To compare trends and undertake statistical analyses of differences in public health performance SERO ( confirmed cases TRANS and fatalities) of Nordic countries; Denmark, Finland, Norway and Sweden, and New Zealand, in response to the COVID-19 pandemic MESHD. Methods: Per capita trends in total cases and per capita fatalities were analysed and difference-in-difference statistical tests undertaken to assess whether differences in stringency of mandated social distancing (SD) measures, testing rates and border closures explain cross-country differences. Results: Sweden is a statistical outlier, relative to its Nordic neighbours, for both per capita cases and per capita fatalities associated with COVID-19 MESHD but not in terms of the reduction in economic growth. Sweden's public health differences, compared to its Nordic neigbours, are partially explained by differences in terms of international border closures and the level of stringency of SD measures (including testing) implemented from early March to June 2020. Conclusions: We find that: one, early imposition of full international travel TRANS restrictions combined with high levels of government-mandated stringency of SD reduced the per capita cases and per capita fatalities associated with COVID-19 MESHD in 2020 in the selected countries and, two, in Nordic countries, less stringent government-mandated SD is not associated with higher quarterly economic growth.

    A comparative study of real-time RT-PCR based SARS-CoV-2 detection methods and its application to human derived and surface swabbed material

    Authors: Aizhan Tastanova; Corinne Isabelle Stoffel; Andreas Dzung; Phil Fang Cheng; Elisa Bellini; Pål Johansen; Agathe Duda; Stefan Nobbe; Reto Lienhard; Philipp Peter Bosshard; Mitchell Paul Levesque; Daniel Muema; Dirhona Ramjit; Gila Lustig; Thumbi Ndung'u; Willem Hanekom; Bernadett I Gosnell; COMMIT-KZN Team; Emily Wong; Tulio de Oliveira; Mahomed-Yunus S Moosa; Alasdair Leslie; Henrik Kloverpris; Alex Sigal

    doi:10.1101/2020.11.23.20236257 Date: 2020-11-24 Source: medRxiv

    Real-time reverse transcription polymerase chain reaction (RT-PCR) remains a gold standard in detection of various viral diseases. In the COVID-19 pandemic MESHD, multiple RT-PCR based tests were developed to screen for viral infection MESHD. As an emergency response to growing testing demand, we established a SARS-CoV-2 PCR diagnostics platform for which we compared different commercial and in-house RT-PCR protocols. We evaluated four commercial (CDC 2019-nCoV, Applied BiosystemsTM 2019-nCoV Assay Kit v1 TF-SinglePlex, 2019-nCoV Assay Kit v2 TF-MultiPlex, and EURORealTime SARS-CoV-2), one customized (Institute Pasteur), and one in-house RT-PCR protocols with 92 SARS-CoV-2 positive and 92 SARS-CoV-2 negative samples. Furthermore, we compared economical and practical characteristics of these protocols. We also developed a highly sensitive digital droplet PCR (ddPCR) method. Finally, we conducted a local environmental study for the presence and infectivity of SARS-CoV-2 on different surfaces in a quarantined household using RT- and ddPCR methods. We found very low limits of detection (1 or 2 viral copies/L), high sensitivities SERO (93.6-97.8%) and specificities (98.7-100%) for the tested RT-PCR protocols. We further demonstrated the feasibility of downscaling two of the commercial protocols, which could optimize testing capacity. In the local environmental study, only one surface sample tested positive for viral RNA, but without detectable infectivity in vitro. Tested commercial and customized RT-PCR detection kits show very good and comparable sensitivity SERO, and specificity, and the kits could be further optimized for use on SARS-CoV-2 viral samples derived from human and surface swabbed samples.

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