Prevalence of respiratory viruses and atypical pathogens in hospitalized children with acute respiratory tract infections: impact of SARS-CoV-2 pandemic in single center in Shanghai / 中华微生物学和免疫学杂志

ABSTRACT

Objective:To investigate the impact of SARS-CoV-2 pandemic on the prevalence of viral pathogens in hospitalized children with acute respiratory tract infections (ARTIs) in Shanghai.Methods:A total of 6 020 throat swab specimens were collected from hospitalized children with ARTIs in Shanghai Children′s Hospital from August 1, 2019 to February 28, 2022. Eleven common respiratory pathogens were detected using multiplex PCR and capillary electrophoresis. Pre-epidemic data referred to the data from August to December, 2019, and the data from August to December, 2020 and August to December, 2021 were used as the post-epidemic data for comparison. Based on the data from March 2020 to February 2022 (the epidemic period), the epidemiology of respiratory pathogens in children with ARTIs in different seasons were compared (spring March to May, summer June to August, autumn September to November, winter December to February of the next year).Results:Of the 6 020 specimens obtained from the patients, 3 753 (62.34%) were positive for at least one pathogen. Human rhinovirus (HRV) was the most commonly detected pathogen (22.76%, 1 442/6 020), followed by human respiratory syncytial virus (HRSV) (16.05%, 966/6 020). From August to December, the detection rate of single respiratory pathogen was 87.94% (569/647) in 2019, 66.21% (480/725) in 2020 and 60.33% (1 075/1 782) in 2021, and the co-infection rate was 25.66% (166/647) in 2019, 9.93% (72/725) in 2020 and 8.87% (158/1 782) in 2021, showing a decreasing trend (χ 2=165.19 and 127.79, P<0.01). Compared with the pre-epidemic period, human metapneumovirus (HMPV), HRV and human parainfluenza virus (HPIV) were the most prevalent pathogens in 2020 [4.97%(36/725), 34.21%(248/725) and 14.48%(105/725); χ 2=26.16, 42.04 and 60.52; P<0.01] and HRSV was the predominant pathogen in 2021 [21.27%(387/1 782), χ 2=44.26, P<0.01]. During the epidemic period, the detection rate of pathogens was 64.49%(1 340/2 078) in 2020, which was significantly higher than that in 2021 [57.48%(1 771/3 081), χ 2=25.43, P<0.01]. Only two respiratory pathogens, Mycoplasma pneumonia and human coronavirus, were detected in the spring of 2020; HRV, human adenovirus and HPIV were detected since the summer of 2020; influenza virus B was detected since the spring of 2021; influenza virus A was detected in only one case in 2020 and other respiratory pathogens were detected since the autumn of 2020. HRV+ HRSV were the main pathogens of co-infections. Conclusions:A series of prevention and control measures taken after the SARS-CoV-2 epidemic caused major changes in the prevalence and the epidemiology of respiratory pathogens in hospitalized children in Shanghai. With the normalization of epidemic prevention and control, the cancellation of strict epidemic prevention policy might lead to the outbreak of some pathogens (HMPV, HRV, HPIV and HRSV) and much attention should be paid to the outbreaks of other respiratory pathogen infections in children.