Speaker
Description
Human rhinovirus (HRV) is the causative agent of > 50% of cold-like illnesses worldwide and responsible for billions of dollars in economic impact each year due to lost productivity. During the 2020-2023 COVID-19 pandemic, strict isolation measures in the initial six months suppressed HRV infections worldwide. Unlike other non-SARS-CoV-2 respiratory viruses, HRV cases returned to pre-pandemic levels in mid-2020, likely due to the reopening of schools in fall 2020 in tandem with the loosening of social restrictions. However, little is known about the impact of these restrictions on the evolutionary history and spatio-temporal dynamics of the virus.
We analyzed the recombination patterns of all publicly available geographical- and time-stamped HRVs -A, -B, and -C full genomes, VP1, and VP4 genes with RDP5. We reconstructed the evolutionary history using a maximum likelihood approach implemented in IQ-Tree.
We obtained 9,225 HRV-A sequences, 1,633 HRV-B sequences, and 6,983 HRV-C sequences from 65 countries worldwide between 1980-2023. Oceania and South America were under-sampled. Kenya (19%), USA (15%), and Germany (12%) submitted the majority of sequences. 84% of sequences were VP4, and only 10% were full genomes. Pre-COVID-19, 15,981 sequences were submitted. During the COVID-19 pandemic, 1,860 sequences were submitted: 56% of the sequences were collected in USA, particularly in Washington and Arizona. Evidence of recombinant sequences was found: 64 for HRV-A full genome, 25 for HRV-B full genome, and 2 for HRV-C VP1. Genomic surveillance was found to peak in times of ongoing respiratory viral outbreaks. Phylogenetic analysis shows geographic intermixing.
Our findings highlight a need for greater genomic surveillance worldwide, particularly in Oceania and South America. We found that surveillance was linked to research efforts in select regions which may bias our understanding of global HRV circulation and evolution. Moreover, the lack of sequencing between 2022-2023 poses a challenge for assessing post-pandemic viral dynamics.
