Trend of respiratory pathogens during the COVID-19 epidemic

Highlights

• •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 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.

1. Introduction

The pandemic caused by the severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) has generated global concern given its rapid spread in multiple countries with fatal progression in a considerable proportion of COVID-19 patients [1,2]. In Italy, the first SARS-CoV-2 infections were diagnosed in Rome, Lazio region, at the end of January 2020, but did not result in COVID-19 spreading. However, the epidemic spreads later, since February 20 in Northern Italy regions, followed by progressive rapid spread to all other areas of the nation. In Lazio region, sustained transmission occurred since the end of February, and COVID-19 testing was initially centralized at the Laboratory of Virology of National Institute for Infectious Diseases “Lazzaro Spallanzani” (INMI) in Rome, designed as regional reference laboratory.

2. Methods

From 1 February to 12 April 2020, 17,164 nasopharyngeal swabs were tested by real time PCR for the presence of SARS-CoV-2. In the same period, coincident with the winter peak of influenza and other respiratory illnesses, 847 samples were analyzed by multiplex PCR assay (QIAstat-Dx Respiratory Panel, Qiagen s.r.l, USA) for the presence of common respiratory pathogens, including Influenza A/B, Parainfluenza 1–4, non-SARS-Coronaviruses, Respiratory Syncytial virus, Adenovirus, Human Metapneumovirus, Rhinovirus/Enterovirus, Bordetella pertussis, Legionella pneumophila, Mycoplasma pneumonia);. In this report, time distribution of positive samples detected for respiratory pathogens during SARS-CoV-2 epidemic, is described.

3. Results

The time trend of SARS-CoV-2 and that of other respiratory pathogens was analyzed by dividing the study period in 2 weeks intervals. The overall frequency of SARS-CoV-2-positive samples was 17.7 %. A low frequency (around 2.5 %) of SARS-CoV-2 RNA-positive samples was observed until weeks 8–9 of 2020, followed by a rapid increase. A peak frequency of 24 % was observed at weeks 10–11, followed by a slight and progressive decline thereafter (22 % at weeks 12–13; 13 % at weeks 14–15) (Fig. 1 A). 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).

Fig. 1.

Trends of SARS-CoV-2 and other respiratory pathogens positive specimens.

(A) Trend of positive SARS-CoV-2 specimens () from week 6 to week 15 of the 2020. (B) Trend of the positive specimens for Influenza A and B (), non-SARS-Coronaviruses () and the other respiratory pathogens () from week 6 to week 15 of the 2020. (C) Trend of the positive specimens for Influenza A and B (), non-SARS-Coronaviruses () and the other respiratory pathogens () from week 6 to week 15 of the 2019. Results are expressed as percentage of positive nasopharyngeal swabs; grey area represents the total number of tested samples.

4. Discussion

Overall, these findings 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, in agreement with the recently published study by Kim et al., highlighting no significant difference in rates of SARS-CoV-2 infection in patients with or without other respiratory pathogens [3].

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.

Funding

This research was supported by funds to National Institute for Infectious Diseases ‘Lazzaro Spallanzani’ IRCCS from: Ministero della Salute, Ricerca Corrente, linea1; European Commission – Horizon 2020 (EU project 101003544 – CoNVat; EU project 101003551 - EXSCALATE4CoV).

Author’s contribution

LB: designed the study, analysed data, contributed in writing and revising the manuscript; EL: assisted in designing the study, analysed data, read and revised manuscript; GS: performed laboratory testing, analysed data, wrote the manuscript; AA: performed laboratory testing, revising the manuscript; MBV: performed laboratory testing; FC: performed laboratory testing; MRC: read and revising the manuscript.

Declaration of Competing Interest

None declared.