Phylogenetic analysis of rhinovirus isolates collected during successive epidemic seasons

Savolainen, Carita; Mulders, Mick N.; Hovi, Tapani

doi:10.1016/s0168-1702(02)00016-3

Cited by 111 publications

(125 citation statements)

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“…We have previously proposed the term 'the closest prototype strain' for assigning the molecular type for HRV field strains (Savolainen et al, 2002b) until more sequence data becomes available and the molecular classification scheme can be agreed. In this study, the clustering of HRV field strain sequences closest to only one of the HRV prototypes was obvious in VP1, but was almost identical in other studied genomic regions.…”

Section: Discussionmentioning

confidence: 99%

“…On: Thu, 10 May 2018 10:00:05 sequencing primers (Lu et al, 2008), those for the VP4/VP2 capsid protein region were 9895 and 9565 (Savolainen et al, 2002b) and those for the VP1 coding region were as described previously (Vlasak et al, 2003). The primers for an approximately 600 nt region spanning the 39 part of the 3D polymerase gene were as described previously (Savolainen et al, 2004).…”

Section: Methodsmentioning

confidence: 99%

“…The global relationships of the HRV field strains were assessed by analysing the VP4/VP2 capsid protein coding region as, at present, most HRV sequence data are available on this region (Kistler et al, 2007a;McErlean et al, 2007;Savolainen et al, 2002b). The HRV field strain VP4/VP2 sequences produced in this study were first aligned with all HRV sequences available in GenBank and the sequences that clustered together with minor receptor group HRV prototype strains were selected for more detailed analysis (Fig.…”

Section: Global Distribution Of Hrv Strainsmentioning

confidence: 99%

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Molecular characterization of human rhinovirus field strains isolated during surveillance of enteroviruses

Blomqvist

Savolainen-Kopra

Paananen

et al. 2009

Journal of General Virology

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Human rhinoviruses (HRVs), which are the most frequent causative agents of acute upper respiratory tract infections, are abundant worldwide. We have identified HRV strains in environmental specimens collected in Finland, Latvia and Slovakia during the surveillance of polioand other enteroviruses. These acid-sensitive HRV strains were isolated under conditions optimized for growth of most of the enteroviruses, i.e. in stationary human rhabdomyosarcoma cells incubated at 36 6C. Phylogenetic analysis of the sequences derived from the partial 59 noncoding region and the capsid region coding for proteins VP4/VP2 and VP1 showed that the HRV field strains clustered together with prototype strains of the HRV minor receptor group. Partial sequences of the 3D polymerase coding region generally followed this pattern, with the exception of a set of three HRV field strains that formed a subcluster not close to any of the established HRV-A types, suggesting that recombination may have occurred during evolution of these HRV strains. Phylogenetic analysis of the VP4/VP2 capsid protein coding region showed that the 'environmental' HRV field strains were practically identical to HRV strains recently sequenced by others in Australia, the United States and Japan. Analysis of amino acids corresponding to the intercellular adhesion molecule-1 receptor footprint in major receptor group HRVs and also in the low-density lipoprotein receptor footprint of minor receptor group HRVs showed conservation of the 'minor receptor group-like' amino acids, indicating that the field strains may have maintained their minor receptor group specificity. INTRODUCTIONHuman rhinoviruses (HRVs) belong to the family Picornaviridae and together with human enteroviruses (HEV) and a number of non-human enterovirus strains comprise the largest genus (Enterovirus) in the family (Knowles, 2008). Clinical illnesses caused by HRV are typically mild and self-limiting upper respiratory tract infections or common colds, but HRVs have also been increasingly associated with other clinical consequences of respiratory tract infection such as acute otitis media (NoksoKoivisto et al., 2004;Pitkaranta et al., 1998;Vesa et al., 2001), acute community-acquired sinusitis (Pitkaranta et al., 1997(Pitkaranta et al., , 2001), bronchiolitis (Hayden, 2004), pneumonia (Papadopoulos, 2004 and exacerbations of existing respiratory disorders such as asthma (Gern, 2002) and chronic obstructive pulmonary disease (Greenberg, 2002).HRV encompasses 100 designated serotypes, including two antigenically distinct subtypes of serotype HRV1 (HRV1A and HRV1B) (Hamparian et al., 1987;Kapikian et al., 1967Kapikian et al., , 1971. The current taxonomy is based on genetic relationships of HRV. Genetic analysis of VP4/VP2 (Savolainen et al., 2002a) and VP1 (Laine et al., 2005; Ledford et al., 2004) capsid protein coding regions showed that the 100 serotypes cluster into two genetically distinct species, HRV-A and HRV-B. One HRV strain originally assigned as HRV87 belongs to the enterovirus species H...

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Global Distribution Of Hrv Strainsmentioning

confidence: 99%

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Molecular characterization of human rhinovirus field strains isolated during surveillance of enteroviruses

Blomqvist

Savolainen-Kopra

Paananen

et al. 2009

Journal of General Virology

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“…5 After excluding influenza A infection (H1N1 2009 and seasonal influenza), the negative samples were tested for the presence of the following viruses as described previously: seasonal influenza virus B (IBV) with primers targeting the NS gene, 6 human rhinovirus (HRV) with primers targeting the 5'NCR and VP4/VP2 genes, 7 human metapneumovirus (hMPV) with primers targeting the fusion protein gene, 8 adenovirus (AdV) with primers targeting the hexon gene 9 and human respiratory syncytial virus (HRSV) with primers targeting the fusion protein gene. 10 The eluted RNA was transcribed into cDNA by moloney murine reverse transcriptase (MMLV-RT; Invitrogen, Carlsbad, CA) using random primers (Invitrogen, Carlsbad, CA) for 1 h at 37°C.…”

Section: Molecular Diagnosticsmentioning

confidence: 99%

Respiratory virus infections among hospitalized patients with suspected influenza A H1N1 2009 virus during the first pandemic wave in Brazil

Watanabe¹,

Carraro²,

Moreira³

et al. 2011

Braz J Infect Dis

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“…Other serotypes detected were HRV‐B27, HRV‐B83, HRV‐B6, and HRV‐B4, all of them also detected in our study. These differences may be due to a specific geographical circulating distribution, as it is described for HRV‐C, 4 or to a distinct seasonal distribution, where several serotypes could circulate in a continuous way, whereas other serotypes could be detected only in specific seasons 17 …”

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confidence: 99%

Spread of different rhinovirus B genotypes in hospitalized children in Spain

Cuevas

Molinero

Pozo

et al. 2012

Influenza Resp Viruses

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Please cite this paper as: Cuevas et al. (2013) Spread of different rhinovirus B genotypes in hospitalized children in Spain. Influenza and Other Respiratory Viruses 7(5), 623–628.Human Rhinovirus (HRV) classification is an evolving process. New genotypes have been described within HRV‐A and HRV‐C species, but only one has been accepted related to HRV‐B. From 2003 to 2010, a total of 3987 nasopharyngeal aspirate samples were taken from pediatric patients admitted to the Severo Ochoa Hospital in Madrid (Spain). After viral analysis, 949 (23·8%) tested positive to HRV. A random selection of 397 (42%) positive samples showed that 39 (9·8%) were HRV‐B. The sequencing of partial VP4/VP2 coding region revealed the spread of 13 of 25 defined HRV‐B serotypes and three putative new genotypes. Such results remark the high diversity of HRV‐B.

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Phylogenetic analysis of rhinovirus isolates collected during successive epidemic seasons

Cited by 111 publications

References 16 publications

Molecular characterization of human rhinovirus field strains isolated during surveillance of enteroviruses

Molecular characterization of human rhinovirus field strains isolated during surveillance of enteroviruses

Respiratory virus infections among hospitalized patients with suspected influenza A H1N1 2009 virus during the first pandemic wave in Brazil

Spread of different rhinovirus B genotypes in hospitalized children in Spain

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