Human rhinoviruses (HRVs; family Picornaviridae), the most frequent causative agents of respiratory infections, comprise more than 100 distinct serotypes. According to previous phylogenetic analysis of the VP4/VP2-coding sequences, all but one of the HRV prototype strains distribute between the two established species, Human rhinovirus A (HRV-A) and Human rhinovirus B (HRV-B). Here, partial sequences of the RNA-dependent RNA polymerase (3D polymerase)-coding gene of 48 HRV prototype strains and 12 field isolates were analysed. The designated division of the HRV strains into the species HRV-A and HRV-B was also seen in the 3D-coding region. Phylogenetically, HRV-B clustered closer to human enterovirus (HEV) species HEV-B, HEV-C and poliovirus than to HRV-A. Intraspecies variation within both HRV-A and HRV-B was greater in the 3D-coding region than in the VP4/VP2-coding region, with the difference maxima reaching 48 % at the nucleotide level and 36 % at the amino acid level in HRV-A and 53 and 35 %, respectively, in HRV-B. Within both species, a few strains formed a separate cluster differing from the majority of strains as much as HEV-B from HEV-C. Furthermore, the tree topology within HRV-A differed from that for VP4/VP2, suggesting possible recombination events in the evolutionary history of the strains. However, all 12 field isolates clustered similarly, as in the capsid region. These results showed that the within-species variation in the 3D region is greater in HRV than in HEV. Furthermore, HRV variation in the 3D region exceeds that in the capsid-coding region.
AlexanderJ. P.Jr,
GaryH. E.Jr,
PallanschM. A.1997; Duration of poliovirus excretion and its implications for acute flaccid paralysis surveillance: a review of the literature. J Infect Dis 175:S176–S182[CrossRef]
ArrudaE.,
PitkärantaA.,
WitekT. J.Jr,
DoyleC. A.,
HaydenF. G.1997; Frequency and natural history of rhinovirus infections in adults during autumn. J Clin Microbiol 35:2864–2868
BlomqvistS.,
SkyttäA.,
RoivainenM.,
HoviT.1999; Rapid detection of human rhinoviruses in nasopharyngeal aspirates by a microwell reverse transcription-PCR-hybridization assay. J Clin Microbiol 37:2813–2816
BlomqvistS.,
SavolainenC.,
RåmanL.,
RoivainenM.,
HoviT.2002; Human rhinovirus 87 and enterovirus 68 represent a unique serotype with rhinovirus and enterovirus features. J Clin Microbiol 40:4218–4223[CrossRef]
BrownB.,
ObersteM. S.,
MaherK.,
PallanschM. A.2003; Complete genomic sequencing shows that polioviruses and members of human enterovirus species C are closely related in the noncapsid coding region. J Virol 77:8973–8984[CrossRef]
HughesP. J.,
NorthC.,
JellisC. H.,
MinorP. D.,
StanwayG.1988; The nucleotide sequence of human rhinovirus 1B: molecular relationships within the rhinovirus genus. J Gen Virol 69:49–58[CrossRef]
HuttunenP.,
SanttiJ.,
PulliT.,
HyypiäT.1996; The major echovirus group is genetically coherent and related to coxsackie B viruses. J Gen Virol 77:715–725[CrossRef]
KamerG.,
ArgosP.1984; Primary structural comparison of RNA-dependent polymerases from plant, animal and bacterial viruses. Nucleic Acids Res 12:7269–7282[CrossRef]
KewO.,
Morris-GlasgowV.,
LandaverdeM.21 other authors2002; Outbreak of poliomyelitis in Hispaniola associated with circulating type 1 vaccine-derived poliovirus. Science 296:356–359[CrossRef]
KingA. M. Q.,
BrownF.,
ChristianP.8 other authors2000; Picornaviruses. In Virus Taxonomy. Seventh Report of the International Committee on Taxonomy of Viruses pp 657–678 Edited by
RegenmortelM. H. V. Van,
FauquetC. M.,
BishopD. H. L.,
CarstensE. B.,
EstesM. K.,
LemonS. M.,
ManiloffJ.,
MayoM. A.,
McGeochD. J.,
PringleC. R.,
WicknerR. B.
San Diego: Academic Press;
LindbergA. M.,
AnderssonP.,
SavolainenC.,
MuldersM. N.,
HoviT.2003; Evolution of the genome of Human enterovirus B : incongruence between phylogenies of the VP1 and 3CD regions indicates frequent recombination within the species. J Gen Virol 84:1223–1235[CrossRef]
MuldersM. N.,
SalminenM.,
KalkkinenN.,
HoviT.2000; Molecular epidemiology of coxsackievirus B4 and disclosure of the correct VP1/2Apro cleavage site: evidence for high genomic diversity and long-term endemicity of distinct genotypes. J Gen Virol 81:803–812
ObersteM. S.,
MaherK.,
KilpatrickD. R.,
FlemisterM. R.,
BrownB. A.,
PallanschM. A.1999a; Typing of human enteroviruses by partial sequencing of VP1. J Clin Microbiol 37:1288–1293
ObersteM. S.,
MaherK.,
KilpatrickD. R.,
PallanschM. A.1999b; Molecular evolution of the human enteroviruses: correlation of serotype with VP1 sequence and application to picornavirus classification. J Virol 73:1941–1948
SavolainenC.,
BlomqvistS.,
MuldersM. N.,
HoviT.2002a; Genetic clustering of all 102 human rhinovirus prototype strains: serotype 87 is close to human enterovirus 70. J Gen Virol 83:333–340
ThompsonJ. D.,
GibsonT. J.,
PlewniakF.,
JeanmouginF.,
HigginsD. G.1997; The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882[CrossRef]
VesaS.,
KleemolaM.,
BlomqvistS.,
TakalaA.,
KilpiT.,
HoviT.2001; Epidemiology of documented viral respiratory infections and acute otitis media in a cohort of children followed from two to twenty-four months of age. Pediatr Infect Dis J 20:574–581[CrossRef]