Table 2_The dynamic etiology and epidemiological patterns of acute respiratory tract infections during and post non-pharmacological interventions of SARS-CoV-2 in Shenzhen, China: a two years’ prospective cohort study from June 2022.docx

BackgroundThe rigorous non-pharmacological interventions (NPIs) during SARS-CoV-2 outbreak posed a deep impact on the etiology and epidemiology of acute respiratory tract infections (ARTIs). We aimed to elucidate the changing patterns during and post NPIs of SARS-CoV-2 in Shenzhen, China.
MethodsA total of 4610 outpatients with ARTIs from the fever clinic of our hospital were enrolled between June 2022 and May 2024, and nasopharyngeal swabs were collected and tested for twenty-five common respiratory pathogens using well-established RT-qPCR. The two year’s period was further divided into three stages: Stage 1 with strict NPIs, Stage 2 with outbreak of SARS-CoV-2 and Stage 3 with regular epidemic of SARS-CoV-2. Demographic and clinical data were also collected and analyzed.
ResultsOverall, 57.05% (2630/4610) of patients were positive for at least one of tested respiratory pathogens, with top five pathogens of IAV (17.09%), H.influenzae (13.97%), SARS-CoV-2 (10.11%), IBV (7.38%) and HAdV (5.66%). Except for SARS-CoV-2, IAV and H.influenzae dominated the three stages, while the other pathogens varied. Meanwhile, positivity rates of most viral pathogens have increased post NPIs. Moreover, HAdV and H.influenzae infections were more frequently found in males. and higher overall rates of viral and bacterial infections were found in both children and the elderly. Notably, the results indicate a higher positivity rate in summer and autumn, with the lowest rate observed in winter. The overall co-infection rate was 24.62%, and the most frequent co-infections were between IAV, SARS-CoV-2, HAdV and H.influenzae.
ConclusionsIn conclusion, the etiology and epidemiological patterns of ARTIs during and post NPIs of SARS-CoV-2 in Shenzhen have changed overtime, and sex, age and seasonal patterns were also found. The findings could provide useful information for the public health measures and the clinical management of respiratory infections.