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      Utility of nasopharyngeal swabs in series before hospitalization during SARS-CoV-2 outbreak

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          Abstract

          Sir, Since the SARS-CoV-2 outbreak, Emergency Departments (EDs) have been through continuous reorganization in order to deal with both COVID-19 and ordinary patients. Nevertheless, previous evidence reports hospitals to be an important source of contagion during epidemic [1,2], making it essential to control the infection risk in healthcare settings. For this reason, and given the reported low sensitivity (63%) of a single test [3], several hospitals decided to require two negative nasopharyngeal swabs before admitting patients to non-COVID wards as has been reported in previous studies regarding MERS-CoV and SARS-CoV-2 [4]. However, such a strategy involves keeping patients in an isolated area awaiting admission, thus increasing boarding and overcrowding. The aim of our study was to analyse the diagnostic yield of a second swab in patients with or without symptoms of COVID-19. We performed a cross-sectional study enrolling all adult patients (i.e. ≥18 years) admitted to the ED of Ospedale Maggiore Policlinico of Milan from March 1 to April 15, 2020 and then hospitalized. Ethical approval for this study was obtained from Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico ethics committee. As suggested by international guidelines [5,6], patients with COVID-19-typical symptoms (fever, dyspnea, cough, sore throat, loss of taste and smell) or close contact with laboratory-confirmed cases were addressed to the COVID-suspected path. Patients without these features were addressed to the non-COVID path. Epidemiological, clinical and laboratory characteristics of the two groups were obtained from electronic medical records. Nasopharyngeal swab specimens were collected following a standardized procedure [7] and RT-PCR was performed on the specimen to detect SARS-CoV-2 RNA. The specimens were processed using GeneFinder COVID-19 Plus RealAmp Kit. In case of a positive test, we admitted patients to a COVID ward; otherwise, we performed a second swab after 24 h. We evaluated the diagnostic yield of the second swab as the proportion of patients with a second positive test on the total number of patients that underwent the second swab and calculated the number needed to diagnose as the ratio between the number of the second swabs performed and the positive ones. We expressed data as proportions and 95% confidence intervals (CIs) and performed all analyses with Microsoft Excel (Microsoft Corporation, Redmond, WA, USA). During the study period, 2721 patients presented to the ED and 835 met the inclusion criteria. Among these, we admitted 630 patients to the COVID-suspected path and 205 to the non-COVID path. In the non-COVID population, we performed a swab in 122 (60%) patients and six (5%; 95% CI: 1%, 9%) patients were positive. Among the 116 negative patients, 61 underwent a second swab within 24 h and 60 patients (98%; 95% CI: 95%, 100%) were negative, while one (2%; 95% CI: 0%, 5%) was positive, so that we had to perform 50 tests to detect one positive patient. In the COVID-suspected population, we tested 579 patients (92%) for SARS-CoV-2 infection: 410 (71%; 95% CI: 67%, 74%) were positive, while 169 (29%; 95% CI: 26%, 33%) were negative. We performed a second swab in 24 h on 89 negative patients among whom 79 patients (89%; 95% CI: 82%, 95%) tested negative and 10 (11%; 95% CI: 5%, 18%) tested positive. Therefore, the number of tests needed to detect one positive patient was nine. All these data are graphically reported in Figure 1 . Figure 1 Patients selected for the study and the results of nasopharyngeal swabs. Figure 1 Our results show that when using swabs in series in patients with low probability of SARS-CoV-2 infection, the second swab has a low diagnostic yield (2%), while when using the second nasal swab as a diagnostic test in patients with a high probability of infection, the diagnostic yield is higher (11%) and may justify performing a second swab in clinical practice. Moreover, considering the overall low sensitivity of the nasopharyngeal swab [6], performing a second swab test does not completely remove the risk of hospitalizing infected patients in non-COVID wards while it increases boarding and overcrowding. In addition, testing patients with two swabs results is an increased financial burden and could lead to difficulties in providing swabs in a context of limited supply of COVID-19 tests. Therefore, we believe that healthcare settings can not rely on the swab test to rule out SARS-CoV-2 infection. Instead, given the high risk of in-hospital contagion, risk control strategies based on personal protective equipment use and preventive isolation for every patient – even when tested negative – is strongly recommended. Author contributions All authors contributed to the design of the study, data collection, analysis and interpretation, revised the article critically and approved the final version. Funding sources This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors. Declaration of Competing Interest None declared.

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          Most cited references 4

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          Detection of SARS-CoV-2 in Different Types of Clinical Specimens

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            Transmission characteristics of MERS and SARS in the healthcare setting: a comparative study

            Background The Middle East respiratory syndrome (MERS) coronavirus has caused recurrent outbreaks in the Arabian Peninsula since 2012. Although MERS has low overall human-to-human transmission potential, there is occasional amplification in the healthcare setting, a pattern reminiscent of the dynamics of the severe acute respiratory syndrome (SARS) outbreaks in 2003. Here we provide a head-to-head comparison of exposure patterns and transmission dynamics of large hospital clusters of MERS and SARS, including the most recent South Korean outbreak of MERS in 2015. Methods To assess the unexpected nature of the recent South Korean nosocomial outbreak of MERS and estimate the probability of future large hospital clusters, we compared exposure and transmission patterns for previously reported hospital clusters of MERS and SARS, based on individual-level data and transmission tree information. We carried out simulations of nosocomial outbreaks of MERS and SARS using branching process models rooted in transmission tree data, and inferred the probability and characteristics of large outbreaks. Results A significant fraction of MERS cases were linked to the healthcare setting, ranging from 43.5 % for the nosocomial outbreak in Jeddah, Saudi Arabia, in 2014 to 100 % for both the outbreak in Al-Hasa, Saudi Arabia, in 2013 and the outbreak in South Korea in 2015. Both MERS and SARS nosocomial outbreaks are characterized by early nosocomial super-spreading events, with the reproduction number dropping below 1 within three to five disease generations. There was a systematic difference in the exposure patterns of MERS and SARS: a majority of MERS cases occurred among patients who sought care in the same facilities as the index case, whereas there was a greater concentration of SARS cases among healthcare workers throughout the outbreak. Exposure patterns differed slightly by disease generation, however, especially for SARS. Moreover, the distributions of secondary cases per single primary case varied highly across individual hospital outbreaks (Kruskal–Wallis test; P 100 cases) for SARS than MERS (2 % versus 1 %); however, owing to higher transmission heterogeneity, the largest outbreaks of MERS are characterized by sharper incidence peaks. The probability of occurrence of MERS outbreaks larger than the South Korean cluster (n = 186) is of the order of 1 %. Conclusions Our study suggests that the South Korean outbreak followed a similar progression to previously described hospital clusters involving coronaviruses, with early super-spreading events generating a disproportionately large number of secondary infections, and the transmission potential diminishing greatly in subsequent generations. Differences in relative exposure patterns and transmission heterogeneity of MERS and SARS could point to changes in hospital practices since 2003 or differences in transmission mechanisms of these coronaviruses. Electronic supplementary material The online version of this article (doi:10.1186/s12916-015-0450-0) contains supplementary material, which is available to authorized users.
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              Epidemic and Emerging Coronaviruses (Severe Acute Respiratory Syndrome and Middle East Respiratory Syndrome)

              Bats are the natural reservoirs of severe acute respiratory syndrome (SARS)-like coronaviruses (CoVs) and likely the reservoir of Middle East respiratory syndrome (MERS)-CoV. The clinical features of SARS-CoV infection and MERS-CoV infection are similar but MERS-CoV infection progresses to respiratory failure more rapidly. Although the estimated pandemic potential of MERS-CoV is lower than that of SARS-CoV, the case fatality rate of MERS is higher. The transmission route and the possibility of other intermediary animal sources remain uncertain among many sporadic primary cases. Clinical trial options for MERS-CoV infection include monotherapy and combination therapy.
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                Author and article information

                Contributors
                Journal
                J Hosp Infect
                J. Hosp. Infect
                The Journal of Hospital Infection
                The Healthcare Infection Society. Published by Elsevier Ltd.
                0195-6701
                1532-2939
                27 June 2020
                27 June 2020
                Affiliations
                [a ]Università degli Studi di Milano, Milan, Italy
                [b ]Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Università degli Studi di Milano, Milan, Italy
                Author notes
                []Corresponding author. Department of Emergency Medicine, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via F. Sforza, 28, 20100 Milan, Italy. . didi.massabo@ 123456gmail.com
                Article
                S0195-6701(20)30317-0
                10.1016/j.jhin.2020.06.032
                7320708
                © 2020 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

                Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.

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                Article

                Infectious disease & Microbiology

                diagnostic yield, sars-cov-2, nasopharyngeal swab

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