Human respiratory viruses, including SARS-CoV-2, circulating in the winter season 2019–2020 in Parma, Northern Italy

Abstract

Graphical abstract

Detection of SARS-CoV-2 and Other Infectious Agents in Lower Respiratory Tract Samples Belonging to Patients Admitted to Intensive Care Units of a Tertiary-Care Hospital, Located in an Epidemic Area, during the Italian Lockdown

“…No co-infection between SARS-CoV-2 and other respiratory viruses was found. This result is in agreement with those reported in the same area in a different period (1 December 2019–31 March 2020) in which among in- and out-patients, viral mixed infections were observed only in three children younger than 1 year old when samples of the upper respiratory tract (two nasopharyngeal swabs and one throat swab) were analyzed [ 18 ].…”

“…The qualitative detection of SARS-CoV-2 RNA was carried out for all samples by using a real-time PCR after reverse transcription (RT-PCR) panel according to the Centers for Disease Control and Prevention (CDC, Atlanta, GA, USA) protocol, with some modifications as previously reported [ 18 ].…”

“…An aliquot of the first sample of each patient was used to detect the nucleic acids of adenovirus, influenza A virus H1 and H3, influenza B virus, parainfluenza virus types 1–4, respiratory syncytial virus types A and B, metapneumovirus, bocavirus types 1–4, rhinovirus types A, B, and C, enterovirus and coronavirus types 229E, NL63 and OC43, with the one-step real-time reverse transcription PCR Allplex™ Respiratory Panels 1–3 assays (Seegene Inc., Seoul, Korea), as described previously [ 18 , 19 ]. In parallel, these samples were also submitted to a rapid cell culture method in 8-well chamber slides (Thermo Fisher Scientific, Monza, Italy) for the detection of influenza A and B viruses, parainfluenza 1-3 viruses and respiratory syncytial virus by indirect immunofluorescence assay (IIF) with monoclonal antibodies (Thermo Fisher Scientific), as previously described [ 19 ].…”

“…In parallel, these samples were also submitted to a rapid cell culture method in 8-well chamber slides (Thermo Fisher Scientific, Monza, Italy) for the detection of influenza A and B viruses, parainfluenza 1-3 viruses and respiratory syncytial virus by indirect immunofluorescence assay (IIF) with monoclonal antibodies (Thermo Fisher Scientific), as previously described [ 19 ]. Moreover, an aliquot of the same samples was also submitted to a conventional cell culture method; when a cytopathic effect was observed, the identification was performed as previously described [ 16 , 18 , 19 ]…”

When the COVID-19 Pandemic Surges during Influenza Season: Lessons Learnt from the Sentinel Laboratory-Based Surveillance of Influenza-Like Illness in Lombardy during the 2019–2020 Season

“…In our ILI series, no SARS-CoV-2-positive cases were identified before week 10-2020, which is in line with the findings obtained in other molecular studies carried out on Italian SARS-CoV-2 strains identified in symptomatic individuals [29][30][31]. On the other hand, ILI surveillance carried out on a greater number of individuals by a larger number of sentinel practitioners may have been able to detect SARS-CoV-2 at an earlier stage of its introduction in Italy, as the first two imported cases were detected at the end of January [32], approximately a month before the first Italian COVID-19 case was reported in Lombardy.…”