key: cord-1005247-f9mpegqj
authors: Sberna, Giuseppe; Amendola, Alessandra; Valli, Maria Beatrice; Carletti, Fabrizio; Capobianchi, Maria Rosaria; Bordi, Licia; Lalle, Eleonora
title: Trend of respiratory pathogens during the covid-19 epidemic
date: 2020-05-26
journal: J Clin Virol
DOI: 10.1016/j.jcv.2020.104470
sha: dda52f1032ae34c2063f6faa2d316023b13d5d6c
doc_id: 1005247
cord_uid: f9mpegqj

In Italy, the first SARS-CoV-2 infections were diagnosed in Rome, Lazio region, at the end of January 2020, but sustained transmission occurred later, since the end of February. From 1 February to 12 April 2020, 17,164 nasopharyngeal swabs were tested by real time PCR for the presence of SARS-CoV-2 at the Laboratory of Virology of National Institute for Infectious Diseases "Lazzaro Spallanzani" (INMI) in Rome. In the same period, coincident with the winter peak of influenza and other respiratory illnesses, 847 samples were analyzed by multiplex PCR assay for the presence of common respiratory pathogens. In our study the time trend of SARS-CoV-2 and that of other respiratory pathogens in the same observation period were analysed. Overall, results obtained suggest that the spread of the pandemic SARS-CoV-2 virus did not substantially affect the time trend of other respiratory infections in our region, highlighting no significant difference in rates of SARS-CoV-2 infection in patients with or without other respiratory pathogens. Therefore, in the present scenario of COVID-19 pandemic, differential diagnosis resulting positive for common respiratory pathogen(s) should not exclude testing of SARS-CoV-2.

 time trend of SARS-CoV-2 and time trend of other respiratory pathogens  SARS-CoV-2 real time RT-PCR  multiplex PCR assay for Respiratory pathogens  SARS-CoV-2 virus did not affect the time trend of other respiratory infections Abstract: In Italy, the first SARS-CoV-2 infections were diagnosed in Rome, Lazio region, at the end of January 2020, but sustained transmission occurred later, since the end of February. From 1 February to 12 April 2020, 17,164 nasopharyngeal swabs were tested by real time PCR for the presence of SARS-CoV-2 at the Laboratory of Virology of National Institute for Infectious Diseases "Lazzaro Spallanzani" (INMI) in Rome. In the same period, coincident with the winter peak of influenza and other respiratory illnesses, 847 samples were analyzed by multiplex PCR assay for the presence of common respiratory pathogens. In our study the time trend of SARS-CoV-2 and that of other respiratory pathogens in the same observation period were analysed. Overall, results obtained suggest that the spread of the pandemic SARS-CoV-2 virus did not substantially affect the time trend of other respiratory infections in our region, highlighting no significant difference in rates of SARS-CoV-2 infection in patients with or without observed at weeks 10-11, followed by a slight and progressive decline thereafter (22% at weeks 12-13; 13% at weeks 14-15) (Fig.1A) . In the same time interval, non-SARS-Coronaviruses were observed in 47 (overall frequency: 5.5%) out of 847 samples, showing a frequency around 7% until weeks 10-11 and a slight flexion during weeks 12-13 (3.8%), reaching 0% thereafter (Fig.1B) . As far as Influenza A and B is concerned, overall frequency was 12.3%, with a frequency of 13% at weeks 6-7, a peak of 25% at weeks 8-9, and a decline thereafter, reaching 0% at weeks 12-15. In the same period, other respiratory pathogens accounted for up to 17% of infections at weeks 6-7, followed by a slight increase at weeks 8-9 (19%), and declining thereafter, until reaching a nadir at weeks 12-13 ( Fig.1B) . A similar trend of non-SARS-Coronaviruses infections was observed in the same period of previous year (Fig.1C ). While in a context of low/absent SARS-CoV-2 circulation, the role of differential diagnosis is crucial, since the detection of alternative pathogen(s) may help to reassure about individual patient's risk of SARS-CoV-2 infection and may inform about the adjustment of public health containment measures 4 , in the present scenario of COVID-19 pandemic, differential diagnosis resulting positive for common respiratory pathogen(s) should not exclude testing of SARS-CoV-2.

Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus-Infected Pneumonia

A Novel Coronavirus from Patients with Pneumonia in China

Rates of Co-infection Between SARS-CoV-2 and Other Respiratory Pathogens

Differential diagnosis of illness in patients under investigation for the novel coronavirus (SARS-CoV-2)

We gratefully acknowledge: