Whole Genome Sequencing of Rhinovirus A49, A47, and A101
To deduce the evolution and circulation patterns of HRV detected in Hong Kong during 2020 – 2021, we sequenced the whole genomes of the three most predominant genotypes (A49, A47, A101) and performed phylogenetic analysis with all publicly available whole genomes from these genotypes in NCBI GenBank. The time of most recent common ancestor (tMRCA) of A49 was 1972 (95% CI: 1940, 1985); the tMRCA of A47 was 1980 (95% CI: 1955, 1985); and the tMRCA of A101 was 1978 (95% CI: 1968, 1986).
Sequenced genomes in Hong Kong revealed six independent transmission lineages (Figure 3 ). Genotype A49, detected during 2020 and 2021, formed two lineages. Except the two A49 viruses detected in 2021 that clustered independently, the rest formed a single lineage with a tMRCA estimated around early 2020. The diversifying pattern of this lineage suggests multiple transmission chains in Hong Kong during 2020 to 2021. In contrast, all 26 A47 genomes, collected during October to December 2020, were highly similar, with a tMRCA just prior to their detection in 2020. The A101 genotype viruses formed three clusters, two of which were detected from October to December 2020 (n = 14 and n = 3) and the other from September to October 2021 (n = 4). While genomes of the two smaller clusters were highly similar, the diversity of the larger cluster dates back to a tMRCA of late 2019. (Figure 3 ).
While no significant correlation was found between HRV genotype and age, most patients presenting with URTIs were positive for HRV A, specifically genotypes A47 (n = 9) and A49 (n = 8). Respiratory symptoms and/or fever were reported in 96% (26/27) of genotype A49 cases; 81% (21/26) of genotype A47 cases; and 57% (12/21) of genotype A101 cases (Table 2 ).