RVdb-Rhinovirus Database

Basic information

Title	New respiratory enterovirus and recombinant rhinoviruses among circulating picornaviruses.
Author	Tapparel, Caroline; Junier, Thomas; Gerlach, Daniel; Van-Belle, Sandra; Turin, Lara; Cordey, Samuel; Muhlemann, Kathrin; Regamey, Nicolas; Aubert, John-David; Soccal, Paola M; Eigenmann, Philippe; Zdobnov, Evgeny; Kaiser, Laurent
Journal	Emerg Infect Dis	Publication Year/Month	2009-May
PMID	19402957	PMCID	PMC2687021
Affiliation	1.University of Geneva Hospitals, Switzerland. caroline.tapparel@hcuge.ch.

Abstract

Rhinoviruses and enteroviruses are leading causes of respiratory infections. To evaluate genotypic diversity and identify forces shaping picornavirus evolution, we screened persons with respiratory illnesses by using rhinovirus-specific or generic real-time PCR assays. We then sequenced the 5 untranslated region, capsid protein VP1, and protease precursor 3CD regions of virus-positive samples. Subsequent phylogenetic analysis identified the large genotypic diversity of rhinoviruses circulating in humans. We identified and completed the genome sequence of a new enterovirus genotype associated with respiratory symptoms and acute otitis media, confirming the close relationship between rhinoviruses and enteroviruses and the need to detect both viruses in respiratory specimens. Finally, we identified recombinants among circulating rhinoviruses and mapped their recombination sites, thereby demonstrating that rhinoviruses can recombine in their natural host. This study clarifies the diversity and explains the reasons for evolution of these viruses.

MeSH terms

*Enterovirus/classification/genetics/isolation & purification

Enterovirus Infections/*epidemiology/virology

Picornaviridae Infections/*epidemiology/virology

*Recombination, Genetic

Respiratory Tract Infections/*epidemiology/virology

*Rhinovirus/classification/genetics/isolation & purification

Adolescent

Adult

Child

Child, Preschool

Genetic Variation

Genotype

Humans

Infant

Infant, Newborn

Molecular Epidemiology

Otitis Media/epidemiology/virology

Phylogeny

Sequence Analysis, DNA

Young Adult

Related RV Strain

StrainID	RV Species	Serotype	Length(nt)	Country	Year	Strain Name
ANC08034	A	96	1773	Switzerland	1999	None
ANC08039	A	82	1761	Switzerland	1999	None
ANC08044	A	76	1779	Switzerland	1999	None
ANC08049	A	67	1728	Switzerland	1999	None
ANC08054	A	61	1785	Switzerland	1999	None
ANC08059	A	55	1524	Switzerland	1999	None
ANC08064	A	49	1716	Switzerland	1999	None
ANC08069	A	43	1668	Switzerland	1999	None
ANC08074	A	34	1629	Switzerland	1999	None
ANC08079	A	29	1857	Switzerland	1999	None
ANC08084	A	20	564	Switzerland	1999	None
ANC08089	A	13	1671	Switzerland	1999	None
ANM08035	A	8	1704	Switzerland	1999	None
ANM08040	A	81	1716	Switzerland	1999	None
ANM08045	A	75	1635	Switzerland	1999	None
ANM08050	A	66	1746	Switzerland	1999	None
ANM08055	A	60	1707	Switzerland	1999	None
ANM08060	A	54	1647	Switzerland	1999	None
ANM08065	A	47	1695	Switzerland	1999	None
ANM08070	A	41	1787	Switzerland	1999	None
ANM08075	A	33	1580	Switzerland	1999	None
ANM08080	A	25	1713	Switzerland	1999	None
ANM08085	A	1	1722	Switzerland	1999	None
ANM08090	A	10	1764	Switzerland	1999	None
ANP08037	A	8	1695	Switzerland	1999	None
ANP08042	A	7	1731	Switzerland	1999	None
ANP08047	A	71	1749	Switzerland	1999	None
ANP08052	A	63	1661	Switzerland	1999	None
ANP08057	A	58	1725	Switzerland	1999	None
ANP08062	A	51	1732	Switzerland	1999	None
ANP08067	A	45	1704	Switzerland	1999	None
ANP08072	A	38	1710	Switzerland	1999	None
ANP08077	A	31	1647	Switzerland	1999	None
ANP08082	A	22	1713	Switzerland	1999	None
ANP08087	A	18	1764	Switzerland	1999	None
ANP08092	A	56	7071	Switzerland	1999	None
ANS08033	A	54	1713	Switzerland	1999	None
ANS08038	A	88	1614	Switzerland	1999	None
ANS08043	A	77	1554	Switzerland	1999	None
ANS08048	A	68	1770	Switzerland	1999	None
ANS08053	A	62	1647	Switzerland	1999	None
ANS08058	A	57	1572	Switzerland	1999	None
ANS08063	A	50	1713	Switzerland	1999	None
ANS08068	A	29	1677	Switzerland	1999	None
ANS08073	A	36	1732	Switzerland	1999	None
ANS08078	A	30	1569	Switzerland	1999	None
ANS08083	A	21	1778	Switzerland	1999	None
ANS08088	A	15	1764	Switzerland	1999	None
ANS09551	A	19	993	Switzerland	1999	CL-039885
ANS09552	A	59	858	Switzerland	1999	CL-080070
ANZ08036	A	90	1725	Switzerland	1999	None
ANZ08041	A	80	1713	Switzerland	1999	None
ANZ08046	A	74	1662	Switzerland	1999	None
ANZ08051	A	65	1778	Switzerland	1999	None
ANZ08056	A	59	1698	Switzerland	1999	None
ANZ08061	A	53	1722	Switzerland	1999	None
ANZ08066	A	46	1773	Switzerland	1999	None
ANZ08071	A	40	1635	Switzerland	1999	None
ANZ08076	A	32	1620	Switzerland	1999	None
ANZ08081	A	23	1722	Switzerland	1999	None
ANZ08086	A	19	1755	Switzerland	1999	None
ANZ08091	A	100	1857	Switzerland	1999	None
BNC01549	B	91	1734	Switzerland	1999	None
BNC01554	B	72	1722	Switzerland	1999	None
BNC01559	B	4	1680	Switzerland	1999	None
BNM01550	B	86	1776	Switzerland	1999	None
BNM01555	B	70	1734	Switzerland	1999	None
BNM01560	B	42	1728	Switzerland	1999	None
BNP01547	B	97	1710	Switzerland	1999	None
BNP01552	B	83	1703	Switzerland	1999	None
BNP01557	B	69	1699	Switzerland	1999	None
BNP01562	B	26	1650	Switzerland	1999	None
BNS01548	B	92	1707	Switzerland	1999	None
BNS01553	B	79	1728	Switzerland	1999	None
BNS01558	B	5	1524	Switzerland	1999	None
BNS01871	B	70	762	Switzerland	1999	CL-Lba236
BNZ01546	B	99	1757	Switzerland	1999	None
BNZ01551	B	84	1719	Switzerland	1999	None
BNZ01556	B	6	1730	Switzerland	1999	None
BNZ01561	B	3	1926	Switzerland	1999	None
CNC05934	C	None	404	Switzerland	2002	CL-QJ274218
CNM05935	C	None	800	Switzerland	2002	CL-QJ274218
CNP05932	C	None	2517	Switzerland	2002	CL-QJ274218
CNS05933	C	None	966	Switzerland	2002	CL-QJ274218
CNS07401	C	None	390	China	2021	RV-C8/HongKong/1395/2021
CNS07402	C	None	390	China	2021	RV-C42/HongKong/1127/2021
CNS07403	C	None	390	China	2021	RV-C42/HongKong/0966/2021
CNS07404	C	None	390	China	2021	RV-C42/HongKong/0946/2021
CNS07405	C	None	376	China	2021	RV-C35/HongKong/2280/2021
CNS07406	C	None	296	Bulgaria	2019	13BG2019
CNS07407	C	None	295	Uruguay		pool.4
CNS07408	C	None	295	Uruguay		pool.1
CNS07409	C	None	294	Bulgaria	2019	23BG2019
CNS07410	C	None	292	Uruguay		3631
CNS07411	C	None	292	Uruguay		3344
CNS07412	C	None	291	Bulgaria	2019	31BG2019
CNS07413	C	None	291	Uruguay		pool.10
CNS07414	C	None	291	Uruguay		3628
CNS07415	C	None	290	Bulgaria	2021	60BG2021
CNS07416	C	None	290	Bulgaria	2021	54BG2021
CNS07417	C	None	290	Bulgaria	2021	47BG2021
CNS07418	C	None	289	Uruguay		3635
CNS07419	C	None	288	Bulgaria	2019	16BG2019
CNS07420	C	None	288	Uruguay		3734
CNS07421	C	None	287	Bulgaria	2019	30BG2019
CNS07422	C	None	286	Bulgaria	2021	61BG2021
CNS07423	C	None	286	Bulgaria	2021	53BG2021
CNS07424	C	None	285	Bulgaria	2021	52BG2021
CNS07425	C	None	284	Bulgaria	2021	58BG2021
CNS07426	C	None	284	Bulgaria	2019	38BG2019
CNS07427	C	None	284	Bulgaria	2019	36BG2019
CNS07428	C	None	279	Bulgaria	2021	63BG2021
CNS07429	C	None	275	Bulgaria	2021	56BG2021
CNS07430	C	None	275	Bulgaria	2021	48BG2021
CNS07431	C	None	273	Bulgaria	2022	64BG2021
CNS07432	C	None	269	Bulgaria	2021	49BG2021
CNZ05931	C	11	7108	Switzerland	2008	CL-170085
CNZ05936	C	19	3055	Switzerland	2003	CL-Fnp5
UNS01154	A	76	6964	Switzerland	1999	CL-135587
UNS01155	Unclassified	None	1349	Switzerland	2007	CL-013775
UNS01156	Unclassified	None	1349	Switzerland	2004	CL-023751
UNS01157	Unclassified	None	1349	Switzerland	2007	CL-029646
UNS01158	Unclassified	None	1349	Switzerland	2004	CL-030103
UNS01159	Unclassified	None	1349	Switzerland	2003	CL-030118
UNS01160	Unclassified	None	1349	Switzerland	2005	CL-030119
UNS01161	Unclassified	None	1349	Switzerland	2006	CL-039885
UNS01162	Unclassified	None	1349	Switzerland	2005	CL-040055
UNS01163	Unclassified	None	1349	Switzerland	2003	CL-043679
UNS01164	Unclassified	None	1346	Switzerland	2001	CL-060043
UNS01165	Unclassified	None	1349	Switzerland	2005	CL-064493
UNS01166	Unclassified	None	1349	Switzerland	2007	CL-070102
UNS01167	Unclassified	None	1349	Switzerland	2007	CL-073908
UNS01168	Unclassified	None	1346	Switzerland	2006	CL-080053
UNS01169	Unclassified	None	1349	Switzerland	1999	CL-080070
UNS01170	Unclassified	None	1352	Switzerland	2004	CL-100091
UNS01171	Unclassified	None	1349	Switzerland	2004	CL-110090
UNS01172	Unclassified	None	1349	Switzerland	1999	CL-1432930
UNS01173	Unclassified	None	1349	Switzerland	1999	CL-1433740
UNS01174	Unclassified	None	1349	Switzerland	2006	CL-144349
UNS01175	Unclassified	None	1349	Switzerland	2006	CL-144350
UNS01176	Unclassified	None	1349	Switzerland	2003	CL-145608
UNS01177	Unclassified	None	1349	Switzerland	1999	CL-155838
UNS01178	Unclassified	None	1349	Switzerland	2007	CL-170122
UNS01179	Unclassified	None	1361	Switzerland	2006	CL-200087
UNS01180	Unclassified	None	1349	Switzerland	2007	CL-210068
UNS01181	Unclassified	None	1349	Switzerland	2003	CL-240132
UNS01182	Unclassified	None	1770	Switzerland	2006	CL-246706
UNS01183	Unclassified	None	1349	Switzerland	2003	CL-274951
UNS01184	Unclassified	None	1349	Switzerland	2007	CL-279529
UNS01185	Unclassified	None	1349	Switzerland	2006	CL-290046
UNS01186	Unclassified	None	1349	Switzerland	2005	CL-310106
UNS01187	Unclassified	None	1346	Switzerland	2004	CL-aaLba1089
UNS01188	Unclassified	None	1346	Switzerland	1999	CL-DY311099
UNS01189	Unclassified	None	1346	Switzerland	2001	CL-elLCT220052
UNS01190	Unclassified	None	1346	Switzerland	2005	CL-Fnp507
UNS01191	Unclassified	None	1346	Switzerland	2006	CL-Fnp543
UNS01192	Unclassified	None	1349	Switzerland	2004	CL-Lba198
UNS01193	Unclassified	None	1346	Switzerland	2004	CL-Lba236
UNS01194	Unclassified	None	1346	Switzerland	2005	CL-Lba503
UNS01195	Unclassified	None	1349	Switzerland	2001	CL-perLCT080057
UNS01196	Unclassified	None	1349	Switzerland	2004	CL-ruLba1009
UNS01197	Unclassified	None	1346	Switzerland	2005	CL-vaFnp389
UNS01198	Unclassified	None	1869	Switzerland	1999	Hanks
UNS01199	A	67	723	Switzerland	1999	CL-013775
UNS01200	A	7	735	Switzerland	1999	CL-023751
UNS01201	A	73	726	Switzerland	1999	CL-029646
UNS01202	A	34	726	Switzerland	1999	CL-030103
UNS01203	Unclassified	None	717	Switzerland	1999	CL-030118
UNS01204	A	1	726	Switzerland	1999	CL-030119
UNS01205	A	75	726	Switzerland	1999	CL-040055
UNS01206	A	54	723	Switzerland	1999	CL-043679
UNS01207	B	27	738	Switzerland	1999	CL-060043
UNS01208	A	34	726	Switzerland	2005	CL-064493
UNS01209	A	78	726	Switzerland	1999	CL-070102
UNS01210	A	67	723	Switzerland	1999	CL-073908
UNS01211	A	46	732	Switzerland	1999	CL-080053
UNS01212	A	61	726	Switzerland	1999	CL-100091
UNS01213	A	61	726	Switzerland	1999	CL-110090
UNS01214	Unclassified	None	714	Switzerland	1999	CL-1432930
UNS01215	A	101	735	Switzerland	1999	CL-1433740
UNS01216	A	94	723	Switzerland	1999	CL-144349
UNS01217	A	94	723	Switzerland	1999	CL-144350
UNS01218	Unclassified	None	714	Switzerland	1999	CL-145608
UNS01219	A	15	726	Switzerland	1999	CL-155838
UNS01220	A	9	723	Switzerland	1999	CL-170122
UNS01221	A	71	735	Switzerland	1999	CL-200087
UNS01222	A	105	720	Switzerland	1999	CL-210068
UNS01223	A	94	723	Switzerland	1999	CL-246706
UNS01224	Unclassified	None	714	Switzerland	2003	CL-240132
UNS01225	Unclassified	None	714	Switzerland	1999	CL-274951
UNS01226	Unclassified	None	717	Switzerland	1999	CL-279529
UNS01227	A	22	723	Switzerland	1999	CL-290046
UNS01228	A	1	726	Switzerland	1999	CL-310106
UNS01229	B	27	738	Switzerland	1999	CL-aaLba1089
UNS01230	Unclassified	None	663	Switzerland	1999	CL-Bern
UNS01231	Unclassified	None	666	Switzerland	1999	CL-DY311099
UNS01232	A	12	726	Switzerland	1999	CL-elLCT220052
UNS01233	A	68	729	Switzerland	1999	CL-Fnp507
UNS01234	A	58	726	Switzerland	1999	CL-Lba198
UNS01235	A	68	729	Switzerland	1999	CL-Lba503
UNS01236	Unclassified	None	666	Switzerland	1999	CL-Lba516
UNS01237	A	64	723	Switzerland	1999	CL-perLCT080057
UNS01238	A	24	720	Switzerland	1999	CL-ruLba1009
UNS01239	B	3	738	Switzerland	1999	CL-vaFnp389
UNS01240	Unclassified	None	861	Switzerland	2007	CL-013775
UNS01241	Unclassified	None	177	Switzerland	2004	CL-023751
UNS01242	Unclassified	None	271	Switzerland	2007	CL-029646
UNS01243	Unclassified	None	175	Switzerland	2004	CL-030103
UNS01244	Unclassified	None	177	Switzerland	2003	CL-030118
UNS01245	Unclassified	None	177	Switzerland	2005	CL-030119
UNS01246	Unclassified	None	271	Switzerland	2006	CL-039885
UNS01247	Unclassified	None	177	Switzerland	2005	CL-040055
UNS01248	Unclassified	None	175	Switzerland	2003	CL-043679
UNS01249	Unclassified	None	176	Switzerland	2001	CL-060043
UNS01250	Unclassified	None	175	Switzerland	2005	CL-064493
UNS01251	Unclassified	None	276	Switzerland	2007	CL-070102
UNS01252	Unclassified	None	862	Switzerland	2007	CL-073908
UNS01253	Unclassified	None	269	Switzerland	2006	CL-080053
UNS01254	Unclassified	None	175	Switzerland	1999	CL-080070
UNS01255	Unclassified	None	177	Switzerland	2004	CL-100091
UNS01256	Unclassified	None	177	Switzerland	2004	CL-110090
UNS01257	Unclassified	None	269	Switzerland	1999	CL-1230139
UNS01258	Unclassified	None	269	Switzerland	1999	CL-1235044
UNS01259	Unclassified	None	270	Switzerland	1999	CL-1236331
UNS01260	Unclassified	None	268	Switzerland	1999	CL-1236333
UNS01261	Unclassified	None	272	Switzerland	1999	CL-1237693
UNS01262	Unclassified	None	268	Switzerland	1999	CL-1432930
UNS01263	Unclassified	None	274	Switzerland	1999	CL-1433740
UNS01264	Unclassified	None	268	Switzerland	1999	CL-1433741
UNS01265	Unclassified	None	272	Switzerland	1999	CL-1434143
UNS01266	Unclassified	None	268	Switzerland	1999	CL-1434714
UNS01267	Unclassified	None	273	Switzerland	1999	CL-1434715
UNS01268	Unclassified	None	275	Switzerland	1999	CL-1438069
UNS01269	Unclassified	None	271	Switzerland	2006	CL-144349
UNS01270	Unclassified	None	271	Switzerland	2006	CL-144350
UNS01271	Unclassified	None	175	Switzerland	2003	CL-145608
UNS01272	Unclassified	None	175	Switzerland	1999	CL-155838
UNS01273	Unclassified	None	269	Switzerland	2007	CL-170122
UNS01274	Unclassified	None	276	Switzerland	2006	CL-200087
UNS01275	Unclassified	None	269	Switzerland	2007	CL-210068
UNS01276	Unclassified	None	175	Switzerland	2003	CL-240132
UNS01277	Unclassified	None	271	Switzerland	2006	CL-246706
UNS01278	Unclassified	None	175	Switzerland	2003	CL-274951
UNS01279	Unclassified	None	272	Switzerland	2007	CL-279529
UNS01280	Unclassified	None	271	Switzerland	2006	CL-290046
UNS01281	Unclassified	None	177	Switzerland	2005	CL-310106
UNS01282	Unclassified	None	267	Switzerland	2004	CL-aaLba1089
UNS01283	Unclassified	None	274	Switzerland	2005	CL-Bern226
UNS01284	Unclassified	None	274	Switzerland	2005	CL-Bern230
UNS01285	Unclassified	None	265	Switzerland	2007	CL-C31
UNS01286	Unclassified	None	269	Switzerland	2007	CL-C33
UNS01287	Unclassified	None	273	Switzerland	2007	CL-C37
UNS01288	Unclassified	None	269	Switzerland	2007	CL-C47
UNS01289	Unclassified	None	269	Switzerland	2007	CL-C51
UNS01290	Unclassified	None	270	Switzerland	2007	CL-C5
UNS01291	Unclassified	None	270	Switzerland	2007	CL-C62
UNS01292	Unclassified	None	182	Switzerland	1999	CL-DY311099
UNS01293	Unclassified	None	270	Switzerland	2001	CL-elLCT220052
UNS01294	Unclassified	None	269	Switzerland	2004	CL-Fnp129
UNS01295	Unclassified	None	267	Switzerland	2004	CL-Fnp260
UNS01296	Unclassified	None	271	Switzerland	2005	CL-Fnp409
UNS01297	Unclassified	None	273	Switzerland	2005	CL-Fnp507
UNS01298	Unclassified	None	271	Switzerland	2006	CL-Fnp543
UNS01299	Unclassified	None	271	Switzerland	2004	CL-Lba198
UNS01300	Unclassified	None	269	Switzerland	2004	CL-Lba202
UNS01301	Unclassified	None	270	Switzerland	2004	CL-Lba236
UNS01302	Unclassified	None	273	Switzerland	2005	CL-Lba503
UNS01303	Unclassified	None	265	Switzerland	2005	CL-Lba516
UNS01304	Unclassified	None	271	Switzerland	2001	CL-perLCT080057
UNS01305	Unclassified	None	272	Switzerland	2004	CL-ruLba1009
UNS01306	Unclassified	None	270	Switzerland	2005	CL-vaFnp389

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