key: cord-331002-7uojryqz
authors: Valent, Francesca; Di Chiara, Antonio
title: Detection of SARS-CoV-2 in nasopharynx according to clinical phenotype of affected patients
date: 2020-09-06
journal: Clin Microbiol Infect
DOI: 10.1016/j.cmi.2020.08.041
sha: 
doc_id: 331002
cord_uid: 7uojryqz

OBJECTIVES: Duration of SARS-CoV-2 in upper respiratory tract is extremely variable, but its relation to disease severity is unknown. We investigated such relation in the 530,000-inhabitant North-Eastern Italian province of Udine. METHODS: We analysed real‐time reverse‐transcriptase polymerase chain reaction (RT-PCR) tests for SARS-CoV-2 on upper respiratory specimens conducted at the Virology Laboratory of the University Hospital of Udine, Italy, serving the whole province, from March 1 to April 30, 2020, on positive subjects of four groups characterized by different disease severity (critically ill patients admitted to Intensive Care Units, patients admitted to Infectious Disease Units, symptomatic patients visited at the Emergency Department and not hospitalized, and asymptomatic subjects tested during contact tracing or screening activities). Duration of viral positivity was assessed from the first positive test to the day of the first of two consecutive negative tests. Univariate and multivariate analyses were conducted to investigate differences in the four groups. RESULTS: From March 1 to April 30, 39,483 RT-PCR tests for SARS-CoV-2 were conducted on 23,778 persons. 974 subjects had a positive test result. Among those with multiple tests (N=878), mean time to negativity was 23.7 days (standard error 0.3639) (median 23, interquartile range: 16-30 days). Mean time to negativity was longer in the ICU group than in the others, whereas no difference was observed between asymptomatic patients and those with mild disease. CONCLUSIONS: Disease control measures should not be adjusted to account for differences in viral shedding according to symptomatic status.

Italian province of Udine. after the first positive test were excluded from further analyses. 90 In each group, time of return to negativity was described through the mean and standard error 91 (SE) and the quartiles. Kaplan-Meier curves were used to describe time to negativity in each group. 92 The log-rank test and Wilcoxon's test were used to assess whether the groups differed significantly. P-93 values<0.05 were considered statistically significant. Finally, Cox regression was used to assess Table 2 shows the distributions of time to negativity in the 4 groups. Mean, median, and 123 maximum values were similar in the asymptomatic, ED, and IDU groups, but they were higher in the 124 ICU group. Figure 1 shows Kaplan-Meier curves for time to negativity in the 4 groups. The curves 125 were not significantly different according to the log-rank test (p-value 0.1020), but they were 126 significantly different according to Wilcoxon's test which is more sensitive to earlier time points (p-127 value 0.0242). 128 The results of Cox regression are illustrated in Table 3 . After adjusting for sex and age, at any 129 time point, ICU patients were less likely to return to negativity than the other patients. Female sex and 130 increasing age were associated with a reduced likelihood of returning to negativity.

The main finding of our study is the long duration of SARS-CoV-2 positivity in a population 133 including patients ranging from asymptomatic to acute respiratory distress syndrome requiring ICU 134 care. For the whole cohort, the median duration is 23 days (with a range from 2 to 53 days). In addition, a standardized method of NP swab collection was adopted. Broncho alveolar lavage 172 or gastric tubage were never used to assess the non-infectiveness of the subject in healing phase. 173 This research has also a number of limitations. Our source of data did not include information 174 on medications used by patients so we cannot say whether any therapeutic agent might have influenced J o u r n a l P r e -p r o o f 

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