Human rhinoviruses (HRV) are the most frequent cause of respiratory infection in humans. These viruses belong to the Picornaviridae, one of the oldest and most diversified human virus family, characterized by a non-enveloped, single positive-stranded RNA genome. Although rhinovirus replication is often restricted to the upper respiratory tract leading to self-limited illnesses of short duration, such as the common cold, HRV can also invade the lower respiratory tract and lead to more serious infections. Similar to many other RNA viruses, the error-prone rhinoviral polymerase can accumulate a large number of nucleotide mutations over a very short period of time, a feature that favors viral adaptation. The error rate of picornavirus RNA polymerases has been estimated to range between 10−3 and 10−4 errors/nucleotide/cycle of replication. This variability is a driving force for virus evolution and results in a large genetic and phenotypic diversity illustrated by the very high number of different HRV serotypes identified to date.
By using ultra-deep sequencing technology, researchers were able to pinpoint HRV evolution at the level of a quasispecies population both in vivo and in vitro. The data illustrate the ability of rhinoviruses to produce several new variants as rapidly as 5 days’ post-infection.
Rhinovirus Genome Evolution during Experimental Human Infection. 2010 PLoS ONE 5(5): e10588. doi:10.1371/journal.pone.0010588
Human rhinoviruses (HRVs) evolve rapidly due in part to their error-prone RNA polymerase. Knowledge of the diversity of HRV populations emerging during the course of a natural infection is essential and represents a basis for the design of future potential vaccines and antiviral drugs. To evaluate HRV evolution in humans, nasal wash samples were collected daily for five days from 15 immunocompetent volunteers experimentally infected with a reference stock of HRV-39. In parallel, HeLa-OH cells were inoculated to compare HRV evolution in vitro. Nasal wash in vivo assessed by real-time PCR showed a viral load that peaked at 48–72 h. Ultra-deep sequencing was used to compare the low-frequency mutation populations present in the HRV-39 inoculum in two human subjects and one HeLa-OH supernatant collected 5 days post-infection. The analysis revealed hypervariable mutation locations in VP2, VP3, VP1, 2C and 3C genes and conserved regions in VP4, 2A, 2B, 3A, 3B and 3D genes. These results were confirmed by classical sequencing of additional samples, both from inoculated volunteers and independent cell infections, and suggest that HRV inter-host transmission is not associated with a strong bottleneck effect. A specific analysis of the VP1 capsid gene of 15 human cases confirmed the high mutation incidence in this capsid region, but not in the antiviral drug-binding pocket. We could also estimate a mutation frequency in vivo of 3.4×10−4 mutations/nucleotides and 3.1×10−4 over the entire ORF and VP1 gene, respectively. In vivo, HRV generate new variants rapidly during the course of an acute infection due to mutations that accumulate in hot spot regions located at the capsid level, as well as in 2C and 3C genes.