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.