Surveillance of rhinovirus diversity among a university community identifies multiple types from all three species including an unassigned rhinovirus A genotype

Abstract

We determine the presence and diversity of rhinoviruses in nasopharyngeal swab samples from 248 individuals who presented with influenza-like illness (ILI) at a university clinic in the Southwest United States between October 1, 2020 and March 31, 2021. We identify at least 13 rhinovirus genotypes (A11, A22, A23, A25, A67, A101, B6, B79, C1, C17, C36, and C56, as well a new genotype [AZ88**]) and 16 variants that contributed to the burden of ILI in the community. We also describe the complete capsid protein gene of a member (AZ88**) of an unassigned rhinovirus A genotype.

Keywords: Southwestern United States; high-throughput nucleotide sequencing; population surveillance; rhinovirus; student health services.

FIGURE 1

Maximum‐likelihood tree of rhinovirus sequences recovered in this study (black squares) and their top five hits in GenBank. The tree was inferred using the VP3 genomic region. Bootstrap values are indicated if greater than 50%. The letters, A, B, and C represent the three different rhinovirus species.

FIGURE 2

Genetic characterization and similarity of rhinoviruses. Maximum‐likelihood tree and pairwise identity analysis of AZ88** VP1, its top 20 BLASTn hits and reference sequences of rhinovirus A7, A36, A58, A88, A89, and A109. Bootstrap values are indicated if greater than 50%. Pairwise identity above and below 88% are colored red and blue, respectively. Please see Table S1 for the pairwise identity data that were used to make the matrix in this figure.