Rhinovirus Genome Variation during Chronic Upper and Lower Respiratory Tract Infections

Abstract

Routine screening of lung transplant recipients and hospital patients for respiratory virus infections allowed to identify human rhinovirus (HRV) in the upper and lower respiratory tracts, including immunocompromised hosts chronically infected with the same strain over weeks or months. Phylogenetic analysis of 144 HRV-positive samples showed no apparent correlation between a given viral genotype or species and their ability to invade the lower respiratory tract or lead to protracted infection. By contrast, protracted infections were found almost exclusively in immunocompromised patients, thus suggesting that host factors rather than the virus genotype modulate disease outcome, in particular the immune response. Complete genome sequencing of five chronic cases to study rhinovirus genome adaptation showed that the calculated mutation frequency was in the range observed during acute human infections. Analysis of mutation hot spot regions between specimens collected at different times or in different body sites revealed that non-synonymous changes were mostly concentrated in the viral capsid genes VP1, VP2 and VP3, independent of the HRV type. In an immunosuppressed lung transplant recipient infected with the same HRV strain for more than two years, both classical and ultra-deep sequencing of samples collected at different time points in the upper and lower respiratory tracts showed that these virus populations were phylogenetically indistinguishable over the course of infection, except for the last month. Specific signatures were found in the last two lower respiratory tract populations, including changes in the 5′UTR polypyrimidine tract and the VP2 immunogenic site 2. These results highlight for the first time the ability of a given rhinovirus to evolve in the course of a natural infection in immunocompromised patients and complement data obtained from previous experimental inoculation studies in immunocompetent volunteers.

Spread of different rhinovirus B genotypes in hospitalized children in Spain

“…A remarkable finding is the high HRV‐B diversity found in our study, with 13 of 25 serotypes detected, compared with other surveys. Studies performed in Edinburgh 6 and Switzerland 13 detected six different serotypes each, while four different types were found in China, 14 South Africa, 15 and the USA, 16 respectively. This lower diversity may be due to the number of years spanned in these studies –usually one or two – compared with our study of a 6·5‐year period.…”

Critical Analysis of Rhinovirus RNA Load Quantification by Real-Time Reverse Transcription-PCR

“…Thanks to numerous clinical studies, data have been gathered regarding implication of HRV in the exacerbation of underlying diseases, such as cystic fibrosis, asthma, and chronic obstructive pulmonary disease (1,3,7,8,10,17,18,20,21,25), as well as concerning the possible impact of a given HRV species on disease severity (9,(11)(12)(13)23). However, there are inconsistent data about whether viral load is correlated with disease severity, and the threshold cycle (C T ) values from real-time RT-PCR are converted too frequently into viral copies per milliliter without any validation.…”

Genomic Applications in the Clinical Management of Infectious Diseases

“…Both 454 pyrosequencing and Illumina platforms have been used. Viral intrahost diversity has been interrogated for a number of viruses, including HIV [ 107 -110 ], infl uenza A [ 95 , 111 -113 ], HCV [ 106 ], dengue virus [ 114 ], rhinovirus [ 115 ], and CMV [ 105 , 116 ] to name a few. Major challenges in characterizing viral variants are sequencing/amplifi cation error correction and haplotype reconstruction, because most platforms produce reads that are shorter than a complete viral genome.…”