Title Phylogenetic analysis of human rhinovirus isolates collected from otherwise healthy children with community-acquired pneumonia during five successive years.
Author Daleno, Cristina; Piralla, Antonio; Scala, Alessia; Senatore, Laura; Principi, Nicola; Esposito, Susanna
Journal PLoS One Publication Year/Month 2013
PMID 24260436 PMCID PMC3833952
Affiliation 1.Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Universita degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.

In order to evaluate the circulation of the different human rhinovirus (HRV) species and genotypes in Italian children with radiographically confirmed community-acquired pneumonia (CAP), a nasopharyngeal swab was obtained from 643 children admitted to hospital because of CAP during five consecutive winter and early spring seasons (2007-2012). Real-time reverse transcriptase polymerase chain reaction (RT-PCR) was used to identify HRV, and the HRV-positive samples were used for sequencing analysis and to reconstruct the phylogenetic tree. HRV was identified in 198 samples (42.2%), and the VP4/VP2 region was successfully amplified in 151 (76.3%). HRV-A was identified in 78 samples (51.6%), HRV-B in 14 (9.3%) and HRV-C in 59 (39.1%). Forty-seven (31.1%) of the children with HRV infection were aged <1 year, 71 (47.0%) were aged 1-3 years, and 33 (21.9%) were aged >/=4 years. Blast and phylogenetic analyses showed that the HRV strains were closely related to a total of 66 reference genotypes, corresponding to 29 HRV-A, 9 HRV-B and 28 HRV-C strains. Nucleotide variability was 37% between HRV-A and HRV-B, 37.3% between HRV-A and HRV-C, and 39.9% between HRV-B and HRV-C. A number of sequences clustered with known serotypes and, within these clusters, there were strains circulating during several seasons. The most frequently detected genotypes were HRV-A78 (n=17), HRV-A12 (n=9) and HRV-C2 (n=5). This study shows that, although it is mainly associated with HRV-A, pediatric CAP can also be diagnosed in subjects infected by HRV-C and, more rarely, by HRV-B. Moreover, a large number of genotypes may be involved in causing pediatric CAP and can be different from year to year. Although the prolonged circulation of the same genotypes can sometimes be associated with a number of CAP episodes in different years.

StrainID RV Species Serotype Length(nt) Country Year Strain Name
ANC06409 A None 393 Italy 2012 MI1052-Mar12
ANC06414 A None 393 Italy 2012 MI646-Feb12
ANC06419 A None 393 Italy 2011 MI101-Feb11
ANC06424 A None 393 Italy 2010 MI24-Dec10
ANC06429 A None 393 Italy 2010 MI1262-Feb10
ANC06434 A None 393 Italy 2009 MI880-Dec09
ANC06439 A None 393 Italy 2009 MI855-Dec09
ANC06444 A None 393 Italy 2009 MI319-Nov09
ANC06449 A None 393 Italy 2009 MI1752-Mar09
ANC06454 A None 393 Italy 2008 MI447-Dec08
ANC06459 A None 393 Italy 2008 MI270-Nov08
ANC06464 A None 393 Italy 2008 MI20139-Mar08
ANC06469 A None 393 Italy 2008 MI20108-Feb08
ANC06474 A None 393 Italy 2008 MI20058-Jan08
ANC06479 A None 393 Italy 2007 MI10113-Dec07
ANM06405 A None 393 Italy 2012 MI3546-Jun12
ANM06410 A None 393 Italy 2012 MI1045-Mar12
ANM06415 A None 393 Italy 2012 MI3526-Jan12
ANM06420 A None 393 Italy 2011 MI96-Feb11
ANM06425 A None 393 Italy 2010 MI1333-Feb10
ANM06430 A None 393 Italy 2010 MI1528-Feb10
ANM06435 A None 393 Italy 2009 MI604-Dec09
ANM06440 A None 393 Italy 2009 MI737-Dec09
ANM06445 A None 393 Italy 2009 MI159-Nov09
ANM06450 A None 393 Italy 2009 MI47-Mar09
ANM06455 A None 393 Italy 2008 MI532-Dec08
ANM06460 A None 393 Italy 2008 MI627-Mar08
ANM06465 A None 393 Italy 2008 MI20143-Mar08
ANM06470 A None 393 Italy 2008 MI10515-Feb08
ANM06475 A None 393 Italy 2008 MI10262-Jan08
ANM06480 A None 393 Italy 2007 MI10055-Dec07
ANP06407 A None 393 Italy 2012 MI3543-May12
ANP06412 A None 384 Italy 2012 MI945-Mar12
ANP06417 A None 393 Italy 2011 MI121-Apr11
ANP06422 A None 393 Italy 2011 MI91-Feb11
ANP06427 A None 393 Italy 2010 MI36-Feb10
ANP06432 A None 393 Italy 2010 MI1208-Jan10
ANP06437 A None 393 Italy 2009 MI943-Dec09
ANP06442 A None 393 Italy 2009 MI787-Dec09
ANP06447 A None 393 Italy 2009 MI956-Dec09
ANP06452 A None 393 Italy 2009 MI1145-Feb09
ANP06457 A None 393 Italy 2008 MI131-Nov08
ANP06462 A None 393 Italy 2008 MI20145-Mar08
ANP06467 A None 393 Italy 2008 MI10633-Mar08
ANP06472 A None 393 Italy 2008 MI10326-Jan08
ANP06477 A None 393 Italy 2008 MI10225-Jan08
ANP06482 A None 393 Italy 2007 MI30-Dec07
ANS06408 A None 393 Italy 2012 MI1108-Mar12
ANS06413 A None 393 Italy 2012 MI944-Mar12
ANS06418 A None 393 Italy 2011 MI117-Mar11
ANS06423 A None 393 Italy 2011 MI89-Feb11
ANS06428 A None 393 Italy 2010 MI1395-Feb10
ANS06433 A None 393 Italy 2010 MI1089-Jan10
ANS06438 A None 393 Italy 2009 MI861-Dec09
ANS06443 A None 393 Italy 2009 MI19-Dec09
ANS06448 A None 393 Italy 2009 MI25-Nov09
ANS06453 A None 393 Italy 2009 MI27-Jan09
ANS06458 A None 393 Italy 2008 MI124-Nov08
ANS06463 A None 393 Italy 2008 MI20158-Mar08
ANS06468 A None 393 Italy 2008 MI10498-Feb08
ANS06473 A None 393 Italy 2008 MI10309-Jan08
ANS06478 A None 393 Italy 2007 MI20004-Dec07
ANZ06406 A None 393 Italy 2012 MI3544-May12
ANZ06411 A None 393 Italy 2012 MI997-Mar12
ANZ06416 A None 393 Italy 2011 MI124-Feb11
ANZ06421 A None 393 Italy 2011 MI92-Feb11
ANZ06426 A None 393 Italy 2010 MI1254-Feb10
ANZ06431 A None 393 Italy 2010 MI1433-Feb10
ANZ06436 A None 393 Italy 2009 MI846-Dec09
ANZ06441 A None 393 Italy 2009 MI691-Dec09
ANZ06446 A None 393 Italy 2009 MI447-Nov09
ANZ06451 A None 393 Italy 2009 MI1384-Feb09
ANZ06456 A None 393 Italy 2008 MI294-Nov08
ANZ06461 A None 393 Italy 2008 MI10720-Mar08
ANZ06466 A None 393 Italy 2008 MI10693-Mar08
ANZ06471 A None 393 Italy 2008 MI20065-Jan08
ANZ06476 A None 393 Italy 2008 MI10251-Jan08
ANZ06481 A None 393 Italy 2007 MI59-Dec07
BNC01184 B None 393 Italy 2012 MI3r58-Mar12
BNC01189 B None 393 Italy 2009 MI152-Nov09
BNC01194 B None 393 Italy 2008 MI20004-Dec08
BNM01185 B None 393 Italy 2010 MI11-Dec10
BNM01190 B None 393 Italy 2009 MI27-Nov09
BNM01195 B None 393 Italy 2008 MI531-Dec08
BNP01187 B None 393 Italy 2010 MI1396-Feb10
BNP01192 B None 393 Italy 2008 MI16-Dec08
BNP01197 B None 393 Italy 2007 MI58-Dec07
BNS01188 B None 393 Italy 2009 MI939-Dec09
BNS01193 B None 393 Italy 2008 MI402-Dec08
BNZ01186 B None 393 Italy 2010 MI1525-Feb10
BNZ01191 B None 393 Italy 2009 MI2009-Apr09
BNZ01196 B None 393 Italy 2007 MI10018-Dec07
CNC04359 C None 387 Italy 2012 MI1107-Mar12
CNC04364 C None 387 Italy 2011 MIbr15-Dec11
CNC04369 C None 387 Italy 2011 MI3507-Dec11
CNC04374 C None 387 Italy 2010 MI1580-Mar10
CNC04379 C None 387 Italy 2009 MI875-Dec09
CNC04384 C None 387 Italy 2009 MI536-Nov09
CNC04389 C None 387 Italy 2009 MI1627-Mar09
CNC04394 C None 387 Italy 2008 MI575-Dec08
CNC04399 C None 387 Italy 2008 MI114-Nov08
CNC04404 C None 387 Italy 2008 MI20132-Mar08
CNC04409 C None 387 Italy 2008 MI20079-Jan08
CNC04414 C None 387 Italy 2007 MI10219-Dec07
CNM04360 C None 387 Italy 2012 MI3533-Feb12
CNM04365 C None 387 Italy 2011 MIbr7-Dec11
CNM04370 C None 387 Italy 2011 MI3506-Dec11
CNM04375 C None 387 Italy 2010 MI1097-Jan10
CNM04380 C None 387 Italy 2009 MI865-Dec09
CNM04385 C None 387 Italy 2009 MI49-Nov09
CNM04390 C None 387 Italy 2009 MI1471-Feb09
CNM04395 C None 387 Italy 2008 MI375-Dec08
CNM04400 C None 387 Italy 2008 MI96-Nov08
CNM04405 C None 387 Italy 2008 MI619-Mar08
CNM04410 C None 387 Italy 2008 MI10239-Jan08
CNM04415 C None 387 Italy 2007 MI10161-Dec07
CNP04357 C None 387 Italy 2012 MI1135-Mar12
CNP04362 C None 387 Italy 2012 MIbr22-Jan12
CNP04367 C None 387 Italy 2011 MIbr19-Dec11
CNP04372 C None 387 Italy 2011 MI62-Jan11
CNP04377 C None 387 Italy 2009 MI653-Dec09
CNP04382 C None 387 Italy 2009 MI28-Dec09
CNP04387 C None 387 Italy 2009 MI26-Nov09
CNP04392 C None 387 Italy 2009 MI1717-Mar09
CNP04397 C None 387 Italy 2008 MI8-Dec08
CNP04402 C None 387 Italy 2008 MI301-Nov08
CNP04407 C None 387 Italy 2008 MI20125-Feb08
CNP04412 C None 387 Italy 2007 MI20011-Dec07
CNS04358 C None 387 Italy 2012 MI1110-Mar12
CNS04363 C None 387 Italy 2011 MI3518-Dec11
CNS04368 C None 270 Italy 2011 MIbr5-Dec11
CNS04373 C None 387 Italy 2010 MI6-Nov10
CNS04378 C None 387 Italy 2009 MI829-Dec09
CNS04383 C None 387 Italy 2009 MI32-Dec09
CNS04388 C None 387 Italy 2009 MI1755-Mar09
CNS04393 C None 387 Italy 2009 MI783-Jan09
CNS04398 C None 258 Italy 2008 MI265-Nov08
CNS04403 C None 387 Italy 2008 MI10563-Mar08
CNS04408 C None 387 Italy 2008 MI10402-Jan08
CNS04413 C None 336 Italy 2007 MI20003-Dec07
CNZ04361 C None 387 Italy 2012 MI684-Feb12
CNZ04366 C None 387 Italy 2011 MI3r1-Dec11
CNZ04371 C None 387 Italy 2011 MI133-Apr11
CNZ04376 C None 387 Italy 2009 MI668-Dec09
CNZ04381 C None 387 Italy 2009 MI817-Dec09
CNZ04386 C None 387 Italy 2009 MI57-Nov09
CNZ04391 C None 387 Italy 2009 MI1793-Mar09
CNZ04396 C None 387 Italy 2008 MI13-Dec08
CNZ04401 C None 387 Italy 2008 MI162-Nov08
CNZ04406 C None 387 Italy 2008 MI20121-Feb08
CNZ04411 C None 387 Italy 2007 MI20021-Dec07
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