Epidemiological shift and clinical characteristics of rhinovirus genotypes in acute respiratory tract infection cases in Kunming, China, from 2019 to 2023

Background: We aimed to investigate the impact of the coronavirus disease 2019 (COVID-19) outbreak on the genetic diversity and clinical severity of rhinovirus (RV) in acute respiratory tract infection (ARTI) cases in Kunming, China. Methods: A total of 25,769 patients with ARTI from September 1, 2019 to December 31, 2023 were enrolled. Patients with COVID-19 were excluded from the study. Nasopharyngeal swabs were collected and screened for RV using multiplex reverse transcription polymerase chain reaction. RV-positive samples underwent nested PCR targeting the VP4/VP2 region. The amplified products were sequenced for genotype identification. Results: A total of 1,017 RV-positive cases were identified (detection rate 3.95%; 1,017/25,769), and all three RV species-RV-A, RV-B, and RV-C-were detected; RV-A was the most prevalent. Overall, 128 distinct RV genotypes, 40 untyped strains, and 1 recombinant strain (A1B) were identified. The predominant genotypes differed between age groups: those <18 years were mainly infected with C-untyped, A36, and A12, whereas those ≥18 years had C1, B52, and A60. Among RV-positive cases, 42.97% were associated with lower respiratory tract infections (LRTI), mainly caused by RV-A and RV-C. RV-C was associated with higher C-reactive protein and procalcitonin. Co-occurrences were recorded in 24.98% (254/1,017) of RV-positive cases and were associated with prolonged hospitalization. RV exhibited no clear seasonal pattern; however, following the COVID-19 outbreak, RV-C was replaced by RV-A. Conclusions: RV remains endemic with significant genetic diversity in the region. The COVID-19 pandemic led to a notable shift in the dominant circulating species from RV-A to RV-C. Emerging mutant strains have contributed to increased disease severity. Both RV-C and RV-A contribute to LRTI in children.