Respiratory viruses are key pathogens that induce ARTIs and are the main cause of hospital admissions and deaths among children in low-income countries [21,22,23]. The rapid development of molecular diagnostic techniques has allowed for the widespread application of multiplex respiratory virus nucleic acid testing methods in clinical practice.

Epidemiological interference among respiratory viruses can affect virus frequency at the host and population levels and interfere with the subsequent frequency and duration of a certain virus or type of virus [24,25,26,27]. Mitigation measures were gradually eased in countries worldwide with the progression of the COVID-19 pandemic over time. Whether the revival of global travel, relaxation of protective measures, and reopening of public places and schools have led to a resurgence in respiratory viruses in children, or whether the lifting of pandemic containment and mitigation measures and the frequency of COVID-19 have interfered with the transmission of other respiratory pathogens are unclear.

The study was based at the First People’s Hospital of Yunnan Province, which has over 2,000 hospital beds and receives more than 2.5 million patients annually. Our results revealed that the overall frequency rate of common respiratory pathogens among children was not significantly affected by the pandemic containment and mitigation measures and remained high throughout the study period. However, the frequency rate determined in this study was considerably higher than the reported rates of 32.1% in Australia [28] and 36% in Xuzhou, China [29], indicating significant regional differences in respiratory pathogen frequency in children. Our results also indicated higher frequency rates in males than in females in 2023, which is inconsistent with findings reported in another study conducted in Guangzhou, China [30].

The most prevalent pathogens differed before and after the lifting of pandemic containment and mitigation measures. The frequency rates of Mp, HADV, and HMPV significantly decreased in 2023, whereas those of influenza-like viruses significantly increased in 2023 compared to 2022, with influenza virus A InfA-H1N1pdm09 and HPIV showing the most notable rebound. The pathogens with the highest frequency rates differed from those reported in other studies conducted in China, which may be attributed to differences in geographical region, study population, and sample size [3, 28]. HRV had the highest frequency rate during the entire study period, which is in agreement with previously reported findings [27]. HRSV frequency negatively correlated with InfA frequency, which is consistent with the results of a study conducted in Germany [31]. At 4 to 6 weeks after the lifting of pandemic containment and mitigation measures, most pathogens exhibited an interruption in frequency. This suggests that the resurgence in SARS-CoV-2 frequency generated a certain degree of interference at the host level, thereby causing a temporary decrease in the susceptibility of the host to viral infections and inducing an immune refractory period toward other pathogens. The specific mechanisms of interference may be related to the sustained upregulation of interferon-stimulated genes, chemokines, and cytokines caused by the frequency of COVID-19 [32].

Children aged 1–3 years had the highest frequency rates, which is consistent with previous findings [3]. Most pathogens exhibited obvious umbrella-shaped distribution characteristics and non-significant differences in frequency before and after the lifting of pandemic containment and mitigation measures. This suggests that the immature immune system of young children may have been insufficient to generate immunity after infection, resulting in a higher tendency for recurrent infections and cross-infections of respiratory pathogens. Interestingly, infants had the lowest infection rates, and most pathogens were undetected in this age group. Further research is necessary to determine whether the unique characteristics of respiratory pathogen infections in infants are related to the immune refractory period caused by immaturity of the immune system. RSV was most common among children aged ≤ 2 years, which is consistent with a previous study [33]. In contrast, the Mp infection rate gradually increased with an increase in age. Our results also indicated the occurrence of a shift in the season of high frequency of HRV, HRSV, and influenza virus A InfA-H3N2. However, further tracking and monitoring will be required to determine whether such shifts in the season of high frequency are temporary or ongoing changes owing to the short duration of the study.

Before December 2022, China had adopted a different response strategy from other countries. SARS-CoV-2 was undetected from week 1 to week 49 in 2022; precise prevention and control prevented the spread of the new coronavirus. Since the lifting of pandemic containment and mitigation measures in December 2022, the frequency of COVID-19 sharply increased and continued to be an epidemic; however, in weeks 1 to 3 of 2023, common respiratory pathogens significantly declined and reached their lowest level. This finding demonstrates the existence of an obvious negative correlation between the frequency of COVID-19 and other pathogens, which is consistent with the finding of a previous study (Fig. 4) [24].

Co-infections with pathogens were mainly dominated by double-pathogen infections; however, the patterns of co-infection became more complex in 2023. It remains unclear whether such changes in co-infection patterns are related to re-entry into the period of high exposure to bacteria and viruses. However, such a phenomenon should receive adequate attention from clinical fields, communities, and epidemic prevention and control authorities. The co-infection rate of HRV was considerably higher than that of all other pathogens and the elucidation of the mechanisms of co-infections is currently a focal topic in research [28]. Screening for SARS-CoV-2 revealed the presence of only six cases of co-infection with SARS-CoV-2 and other pathogens, which again demonstrates the existence of viral interference between COVID-19 frequency and other pathogens.

Despite our promising results, this study also had certain limitations. (1) The study was confined to Kunming, China, which could limit the generalizability of the findings to other regions with different climatic and population characteristics. Clinical and epidemiologic features of some other diseases may be linked to the geographic regions associated with the subjects [34, 35]. (2) Only a limited range of respiratory pathogens were included in the study, which may not encompass all bacteria and viruses that cause respiratory tract symptoms in children and those that are detected using other diagnostic tools, e.g., culture, antigen testing, and sequencing [36,37,38,39,40,41]. (3) Samples were collected from a single hospital over a short period, so studies with a longer study period and wider sample range will be conducted in the future to fully capture long-term trends and epidemiological shifts.

The present study, for the first time, presents valuable insights into the changes in the types and frequency patterns of common respiratory pathogens in children with ARTIs in Kunming during the post-COVID-19 pandemic period under the influence of changes in pandemic prevention and control measures and interference caused by the COVID-19 pandemic. These findings enhance our understanding of the interactions among respiratory pathogens, serve as valuable data for this unique historical period, and are of great significance for the effective control of RTIs and the reduction of the harm caused to pediatric health by respiratory pathogens.