Results
Respiratory virus surveillance of paediatric patients admitted to Queen Mary Hospital, Hong Kong between August 2020 – October 2021 identified 215/2,992 (13.9%) patients with real-time RT-PCR positive samples. Positive specimen types included nasopharyngeal swabs (n = 207), nasopharyngeal aspirates (n = 6), combined nasopharyngeal aspirates and throat swabs (n = 1), and a tracheal aspirate (n = 1). Enterovirus/rhinovirus (n = 178, 85%) was most commonly detected, followed by adenovirus (n = 21), RSV (n = 7), HPIV 1 (n = 3), HPIV 4 (n = 5), HPIV 3 (n = 4), HPIV 2 (n = 1), human coronavirus 229E (n = 2), influenza A (n = 1), human coronavirus HKU-1 (n = 1), and HPMV (n = 1) (Figure 1a ). Seven samples were coinfected with two or more respiratory viruses (Table 1 ). The median age of children that tested positive for any respiratory virus was two years (range: 24 days to 15 years). Upper respiratory tract infection (URTI) was reported at time of sample collection for 47 of the 215 patients that tested positive (median age: 2 years old; range: 24 days to 15 years). Most URTI cases were positive for enterovirus/rhinovirus (41/47, 87%), and the majority of these cases occurred among children between the ages of one and six.
Respiratory virus detections increased rapidly as schools fully reopened in late 2020, peaking at 35 cases per month during November, as reported previously (23), followed by a rapid decline in cases from December 2020 – April 2021 (Figure 1a ). The decline coincides with the fourth wave of COVID-19 infections in Hong Kong (41) and territory-wide school dismissals (Figure 1a ). Following the relaxation of those control measures in the Spring of 2021, cases surged and remained elevated through October 2021. Increases in respiratory virus detection were predominantly associated with increases in enterovirus/rhinovirus. However, a greater viral diversity was captured between February – April 2021 compared to other periods, including cases of human coronaviruses HKU-1 and 229E, HPMV, RSV B, and HPIV 1–4. When face-to-face teaching resumed in March 2021, the number and diversity of viruses detected further increased (Figure 1a ).
HRV VP4/2 gene sequencing identified HRV A (n = 98), B (n = 7) and C (n = 50), while the remaining enterovirus/rhinovirus PCR positive samples (n = 23) could not be sequenced (Figure 1b ). Genotyping revealed that while HRV A caused the spike in November 2020, both HRV A and C were predominantly circulating since May 2021. Maximum likelihood phylogenetic analysis identified 19 independent genotypes, with strong genetic clustering within each of the genotypes in Hong Kong (Figure 2 ). The largest clusters of HRV A genotypes were A49 (n = 27), A47 (n = 26), and A101 (n = 21). A49 was detected throughout the study, except from December 2020 to February 2021, with a peak of 13 cases in May 2021 (Figure 1b ). A47 was detected up to December 2020, and A101 was detected in Autumn 2020 and 2021. Both A47 and A101 peaked in November 2020, with 22 and 11 cases respectively (Figure 1b ). The most diverse circulation of HRV genotypes was observed in the summer of 2021, with 11 genotypes in cocirculation.
Phylogenetic analysis showed that the dominant genotypes detected in our study shared close relationships with viruses collected from Thailand in 2020 and USA in 2021. HRV A49 and A101 shared close relationships with samples from USA in 2021. HRV A19 formed two monophyletic clades, each forming a sister clade with 2020 samples from Thailand. The A47 sequences clustered within a clade that included sequences from USA in 2021, Thailand in 2020, and Malaysia in 2018. HRV C8 and C27 sequences were most closely related to samples collected from Thailand in 2018 and USA in 2021 respectively.