Arch Virol (2003) 148: 2397–2418
The human rhinovirus internal cis-acting replication element
(cre) exhibits disparate properties among serotypes
K. L. McKnight
Department of Microbiology and Immunology, The University of Texas
Medical Branch at Galveston, Galveston, Texas, U.S.A. and Infectious Diseases
Research, Lilly Research Laboratories, LCC Eli Lilly
and Company Indianapolis, Indiana, U.S.A.
Received March 21, 2003; accepted June 9, 2003
Published online September 19, 2003
Summary. It has been reported previously that the Human rhinovirus 14 (HRV-
14) RNA genome contains a cis-acting replication element (cre) that maps to
the capsid coding (P1) sequence . Further characterization of the HRV-14
cre in the present study established that by moving the cre stem-loop structure
downstream, adjacent to the 3
NCR, that its position is not critical for function.
When the P1 sequences of two closely related serotypes of HRV-14 were analyzed
for the presence of a cre, both HRV-3 and HRV-72 were found to contain similar
sequence at the same positions as HRV-14. Moreover, sequence at these positions
produced structures from MFOLD analysis that closely resembled the HRV-14
cre. It was also discovered that neither HRV serotypes 1a or 16 harbor replication
elements that map to the P1 segments of their genomes. Computer and mutational
analyses suggest that the cre in these latter HRV serotypes map instead to the 2A
gene, as has been reported for HRV-2. The putative HRV-3 cre was determined to
be unable to support replication when placed in an HRV-14 replicon background.
Similarly, the previously identiﬁed HRV-2 cre was unable to support replication
of the HRV-14 genome. This ﬁnding is in contrast to the cardiovirus cre, which
has been shown to be functionally active between two members of its family,
and further suggests that there is a close link between the evolution of the human
rhinoviruses and the mechanisms of RNA replication.
Subgenomic (replicon) RNAs derived from infectious cDNA clones of picor-
navirus genomes have been used extensively to study viral RNA replication
[3, 5, 12, 18, 19, 28, 44, 45]. In most conﬁgurations, the P1 (capsid) segment of