Genotyping of human rhinovirus in adult patients with acute respiratory infections identified predominant infections of genotype A21

Abstract

Human rhinovirus (HRV) is an important causative agent of acute respiratory tract infections (ARTIs). The roles of specific HRV genotypes in patients suffering from ARTIs have not been well established. We recruited 147 adult inpatients with community-acquired pneumonia (CAP) and 291 adult outpatients with upper ARTIs (URTIs). Respiratory pathogens were screened via PCR assays. HRV was detected in 42 patients, with 35 species A, five B and two C. Seventeen genotypes were identified, and HRV-A21 ranked the highest (9/42, 21.4%). The HRV-A21-positive infections were detected in four patients with CAP and in five with URTIs, all without co-infections. The HRV-A21 genome sequenced in this study contained 12 novel coding polymorphisms in viral protein (VP) 1, VP2 EF loop, VP3 knob and 3D regions. The infections of HRV-A21 virus obtained in this study could not be neutralized by antiserum of HRV-A21 prototype strain (VR-1131), indicating remarkable antigenic variation. Metagenomic analysis showed the HRV-A21 reads were dominant in bronchoalveolar lavage fluid of the three HRV-A21-positive patients with severe CAP, in which two dead. Our results highlight an unexpected infection of genotype HRV-A21 in the clinic, indicating the necessity of precise genotyping and surveillance of HRVs to improve the clinical management of ARTIs.

Figure 1. Phylogenic analysis and coding polymorphisms of HRV-A21.

(A) The strains identified in this study (dark circles), reference sequences (triangles), and outgroup sequences were analyzed, and phylogenic trees of the genomes and viral protein gene (VP) 1 sequences were constructed using the neighbor-joining method (Kimura’s two-parameter) with 1,000 bootstrap values. (B) Coding polymorphisms in VP1, the VP2 EF loop, and the VP3 knob regions.

Figure 2. Profiles of the microbial species present in lower respiratory tract samples from patients with severe CAP patients analyzed by deep sequencing.

The percentage of microbial species in (A) the bronchoalveolar lavage fluid (BALF) taken on days 4 and 6 of patient RMH123 after the onset of symptoms; (B) the BALF taken on days 12 and 14 of patient RMH114; and (C) the tracheal aspirates taken on days 3 and 5 of patient RMH001, which demonstrates the percentage of rhinovirus reads in most samples.