Title Screening respiratory samples for detection of human rhinoviruses (HRVs) and enteroviruses: comprehensive VP4-VP2 typing reveals high incidence and genetic diversity of HRV species C.
Author Wisdom, A; Leitch, E C McWilliam; Gaunt, E; Harvala, H; Simmonds, P
Journal J Clin Microbiol Publication Year/Month 2009-Dec
PMID 19828751 PMCID PMC2786677
Affiliation 1.Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, United Kingdom.

Rhinovirus infections are the most common cause of viral illness in humans, and there is increasing evidence of their etiological role in severe acute respiratory tract infections (ARTIs). Human rhinoviruses (HRVs) are classified into two species, species A and B, which contain over 100 serotypes, and a recently discovered genetically heterogeneous third species (HRV species C). To investigate their diversity and population turnover, screening for the detection and the genetic characterization of HRV variants in diagnostic respiratory samples was performed by using nested primers for the efficient amplification of the VP4-VP2 region of HRV (and enterovirus) species and serotype identification. HRV species A, B, and C variants were detected in 14%, 1.8%, and 6.8%, respectively, of 456 diagnostic respiratory samples from 345 subjects (6 samples also contained enteroviruses), predominantly among children under age 10 years. HRV species A and B variants were remarkably heterogeneous, with 22 and 6 different serotypes, respectively, detected among 73 positive samples. Similarly, by using a pairwise distance threshold of 0.1, species C variants occurring worldwide were provisionally assigned to 47 different types, of which 15 were present among samples from Edinburgh, United Kingdom. There was a rapid turnover of variants, with only 5 of 43 serotypes detected during both sampling periods. By using divergence thresholds and phylogenetic analysis, several species A and C variants could provisionally be assigned to new types. An initial investigation of the clinical differences between rhinovirus species found HRV species C to be nearly twice as frequently associated with ARTIs than other rhinovirus species, which matches the frequencies of detection of respiratory syncytial virus. The study demonstrates the extraordinary genetic diversity of HRVs, their rapid population turnover, and their extensive involvement in childhood respiratory disease.

StrainID RV Species Serotype Length(nt) Country Year Strain Name
UNS02185 Unclassified None 435 United Kingdom 2006 Resp_2433
UNS02186 Unclassified None 435 United Kingdom 2006 Resp_2437
UNS02187 Unclassified None 435 United Kingdom 2006 Resp_2445
UNS02188 Unclassified None 435 United Kingdom 2006 Resp_2541
UNS02189 Unclassified None 435 United Kingdom 2006 Resp_2542
UNS02190 Unclassified None 435 United Kingdom 2006 Resp_2562
UNS02191 Unclassified None 435 United Kingdom 2006 Resp_2455
UNS02192 Unclassified None 435 United Kingdom 2006 Resp_2456
UNS02193 Unclassified None 435 United Kingdom 2006 Resp_2457
UNS02194 Unclassified None 435 United Kingdom 2006 Resp_2516
UNS02195 Unclassified None 435 United Kingdom 2006 Resp_2663
UNS02196 Unclassified None 435 United Kingdom 2007 Resp_3819
UNS02197 Unclassified None 435 United Kingdom 2007 Resp_4040
UNS02198 Unclassified None 435 United Kingdom 2007 Resp_4110
UNS02199 Unclassified None 435 United Kingdom 2006 Resp_2432
UNS02200 Unclassified None 435 United Kingdom 2006 Resp_2435
UNS02201 Unclassified None 435 United Kingdom 2006 Resp_2436
UNS02202 Unclassified None 435 United Kingdom 2006 Resp_2438
UNS02203 Unclassified None 435 United Kingdom 2006 Resp_2443
UNS02204 Unclassified None 435 United Kingdom 2006 Resp_2449
UNS02205 Unclassified None 435 United Kingdom 2006 Resp_2452
UNS02206 Unclassified None 435 United Kingdom 2006 Resp_2469
UNS02207 Unclassified None 435 United Kingdom 2006 Resp_2473
UNS02208 Unclassified None 435 United Kingdom 2006 Resp_2475
UNS02209 Unclassified None 435 United Kingdom 2006 Resp_2479
UNS02210 Unclassified None 435 United Kingdom 2006 Resp_2495
UNS02211 Unclassified None 435 United Kingdom 2006 Resp_2500
UNS02212 Unclassified None 410 United Kingdom 2006 Resp_2506
UNS02213 Unclassified None 435 United Kingdom 2006 Resp_2507
UNS02214 Unclassified None 435 United Kingdom 2006 Resp_2508
UNS02215 Unclassified None 435 United Kingdom 2006 Resp_2515
UNS02216 Unclassified None 435 United Kingdom 2006 Resp_2518
UNS02217 Unclassified None 434 United Kingdom 2006 Resp_2524
UNS02218 Unclassified None 435 United Kingdom 2006 Resp_2529
UNS02219 Unclassified None 435 United Kingdom 2006 Resp_2530
UNS02220 Unclassified None 435 United Kingdom 2006 Resp_2533
UNS02221 Unclassified None 435 United Kingdom 2006 Resp_2538
UNS02222 Unclassified None 435 United Kingdom 2006 Resp_2540
UNS02223 Unclassified None 435 United Kingdom 2006 Resp_2548
UNS02224 Unclassified None 435 United Kingdom 2006 Resp_2561
UNS02225 Unclassified None 435 United Kingdom 2006 Resp_2564
UNS02226 Unclassified None 435 United Kingdom 2006 Resp_2565
UNS02227 Unclassified None 435 United Kingdom 2006 Resp_2581
UNS02228 Unclassified None 435 United Kingdom 2006 Resp_2591
UNS02229 Unclassified None 435 United Kingdom 2006 Resp_2656
UNS02230 Unclassified None 435 United Kingdom 2007 Resp_3829
UNS02231 Unclassified None 435 United Kingdom 2007 Resp_3833
UNS02232 Unclassified None 435 United Kingdom 2007 Resp_3844
UNS02233 Unclassified None 402 United Kingdom 2007 Resp_3853
UNS02234 Unclassified None 435 United Kingdom 2007 Resp_3857
UNS02235 Unclassified None 435 United Kingdom 2007 Resp_3861
UNS02236 Unclassified None 435 United Kingdom 2007 Resp_3867
UNS02237 Unclassified None 435 United Kingdom 2007 Resp_3881
UNS02238 Unclassified None 435 United Kingdom 2007 Resp_3888
UNS02239 Unclassified None 435 United Kingdom 2007 Resp_3894
UNS02240 Unclassified None 435 United Kingdom 2007 Resp_3915
UNS02241 Unclassified None 435 United Kingdom 2007 Resp_3917
UNS02242 Unclassified None 435 United Kingdom 2007 Resp_3932
UNS02243 Unclassified None 435 United Kingdom 2007 Resp_3936
UNS02244 Unclassified None 435 United Kingdom 2007 Resp_3944
UNS02245 Unclassified None 435 United Kingdom 2007 Resp_3949
UNS02246 Unclassified None 435 United Kingdom 2007 Resp_3953
UNS02247 Unclassified None 435 United Kingdom 2007 Resp_3960
UNS02248 Unclassified None 435 United Kingdom 2007 Resp_3973
UNS02249 Unclassified None 435 United Kingdom 2007 Resp_3990
UNS02250 Unclassified None 435 United Kingdom 2007 Resp_3997
UNS02251 Unclassified None 435 United Kingdom 2007 Resp_3999
UNS02252 Unclassified None 435 United Kingdom 2007 Resp_4002
UNS02253 Unclassified None 435 United Kingdom 2007 Resp_4010
UNS02254 Unclassified None 435 United Kingdom 2007 Resp_4018
UNS02255 Unclassified None 435 United Kingdom 2007 Resp_4022
UNS02256 Unclassified None 435 United Kingdom 2007 Resp_4044
UNS02257 Unclassified None 435 United Kingdom 2007 Resp_4053
UNS02258 Unclassified None 435 United Kingdom 2007 Resp_4073
UNS02259 Unclassified None 435 United Kingdom 2007 Resp_4087
UNS02260 Unclassified None 435 United Kingdom 2007 Resp_4103
UNS02261 Unclassified None 435 United Kingdom 2007 Resp_4117
UNS02262 Unclassified None 435 United Kingdom 2007 Resp_4129
UNS02263 Unclassified None 435 United Kingdom 2007 Resp_4146
UNS02264 Unclassified None 429 United Kingdom 2006 Resp_2453
UNS02265 Unclassified None 429 United Kingdom 2006 Resp_2480
UNS02266 Unclassified None 429 United Kingdom 2006 Resp_2494
UNS02267 Unclassified None 429 United Kingdom 2006 Resp_2503
UNS02268 Unclassified None 429 United Kingdom 2006 Resp_2512
UNS02269 Unclassified None 429 United Kingdom 2006 Resp_2514
UNS02270 Unclassified None 397 United Kingdom 2006 Resp_2526
UNS02271 Unclassified None 429 United Kingdom 2006 Resp_2547
UNS02272 Unclassified None 429 United Kingdom 2006 Resp_2659
UNS02273 Unclassified None 429 United Kingdom 2007 Resp_3832
UNS02274 Unclassified None 429 United Kingdom 2007 Resp_3837
UNS02275 Unclassified None 429 United Kingdom 2007 Resp_3839
UNS02276 Unclassified None 429 United Kingdom 2007 Resp_3856
UNS02277 Unclassified None 427 United Kingdom 2007 Resp_3897
UNS02278 Unclassified None 429 United Kingdom 2007 Resp_3898
UNS02279 Unclassified None 429 United Kingdom 2007 Resp_3901
UNS02280 Unclassified None 429 United Kingdom 2007 Resp_3911
UNS02281 Unclassified None 429 United Kingdom 2007 Resp_3922
UNS02282 Unclassified None 429 United Kingdom 2007 Resp_3938
UNS02283 Unclassified None 417 United Kingdom 2007 Resp_3967
UNS02284 Unclassified None 429 United Kingdom 2007 Resp_3972
UNS02285 Unclassified None 429 United Kingdom 2007 Resp_3993
UNS02286 Unclassified None 429 United Kingdom 2007 Resp_3995
UNS02287 Unclassified None 429 United Kingdom 2007 Resp_4037
UNS02288 Unclassified None 429 United Kingdom 2007 Resp_4051
UNS02289 Unclassified None 429 United Kingdom 2007 Resp_4097
UNS02290 Unclassified None 402 United Kingdom 2007 Resp_4098
UNS02291 Unclassified None 429 United Kingdom 2007 Resp_4101
UNS02292 Unclassified None 429 United Kingdom 2007 Resp_4116
UNS02293 Unclassified None 429 United Kingdom 2007 Resp_4122
UNS02294 Unclassified None 429 United Kingdom 2007 Resp_4123
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