New complete genome sequences of human rhinoviruses shed light on their phylogeny and genomic features

Here we report complete genome sequences of 12 HRV-A and HRV-B serotypes, more than doubling the current number of available HRV sequences. The whole-genome maximum-likelihood phylogenetic analysis suggests that HRV-B and human enteroviruses (HEV) diverged from the last common ancestor after their separation from HRV-A. On the other hand, compared to HEV, HRV-B are more related to HRV-A in the capsid and 3B-C regions. We also identified the presence of a 2C cis-acting replication element (cre) in HRV-B that is not present in HRV-A, and that had been previously characterized only in HEV. In contrast to HEV viruses, HRV-A and HRV-B share also markedly lower GC content along the whole genome length.Our findings provide basis to speculate about both the biological similarities and the differences (e.g. tissue tropism, temperature adaptation or acid lability) of these three groups of viruses.Human rhinovirus (HRV) is the most frequent cause of infection across all age groups of the population [1]. Replication is often restricted to the upper respiratory tract leading to self-limited illnesses such as the common cold. However, HRV infections can also exacerbate pre-existing airway disorders, invade the lower respiratory tract and lead to serious complications [2,3].HRVs are single positive-stranded RNA viruses of approximately 7200 base pairs. They belong to the Picornaviridae family and are closely related to HEVs, another genus of the same family. The genome organization of Picornaviridae is conserved among the family with a long 5'-untranslated region (UTR), a single open reading frame (ORF) encoding a polyprotein, a short 3'UTR, and a poly(A) tail [4]. The 5'-terminal UMP of the viral RNA is covalently linked to the small viral protein VPg [5]. The 5'UTR contains two structural elements [6]. One is the 5'-cloverleaf structure involved in the plus-strand RNA synthesis and in the process of switching from translation to replication [7,8]. The other is the internal ribos