ELUCIDATING HUMAN RHINOVIRUS TRANSMISSION PATHWAYS AT DIFFERING SCALES OF SOCIAL ORGANISATION USING SEQUENCE DATA

Abstract

Background: Human rhinovirus (HRV) is a common viral agent associated with high diversity and a broad spectrum of respiratory disease. Its epidemiological understanding is currently restricted to observations on the circulation of types. We sought to (i) improve understanding of HRV transmission dynamics using partial genome sequences at four scales: a school, neighbouring households, outpatient clinics within the Kilifi Health and Demographic Surveillance System (KHDSS), and hospital inpatients at a countrywide level (ii) design a new sequencing method for HRV whole genome sequencing (WGS) and (iii) compare inferences made from partial and WGS analysis. Methods: This study used previously generated VP4/2 nucleotide sequences of four purposively selected genotypes (66 HRV-A15, 44 HRV-A22, 10 HRV-A101 and 40 HRV-C35) and whole genome sequences (10 HRV-A101, 54 HRV-A15) generated using a newly designed method. Genotype-specific primers were designed to amplify eight DNA amplicons across the entire 7.2 kb genome. Transmission was inferred using Bayesian phylogenetics, haplotype and spatial networks. Results: Phylogenetic inference using partial genomes indicated that sequences mainly clustered by geographical region. Household sequences had the highest sequence identity (99.9%, collected over six months), while those from the country level had the lowest sequence identity (93.0%, collected over 12 months). The newly-designed sequencing method successfully generated 10/10 HRV-A101 and 54/66 HRV-A15 whole genomes. Phylogenetic branching patterns using WGS analysis had higher statistical support than partial sequences. Recombination scans on the full genomes revealed potential breakpoints at the VP3 and 2C regions. Discussion and Conclusion: HRV is characterized by the circulation of minimal intra-type variants at the household level, indicating few introductions. Co-circulation of intra-type vi variants at the KHDSS and country-level suggests multiple virus introductions at larger geographical spaces. The new sequencing method that can enrich HRV in clinical samples for successful WGS, which provided further insight on evolutionary dynamics such as recombination. Further studies should incorporate more types for generalizable findings.