Biomedical subjects

Soile Blomqvist

Publications and source records attributed to Soile Blomqvist.

12 recordsLinked to original sources

PubMed2006

Alignment of capsid protein VP1 sequences of all human rhinovirus prototype strains: conserved motifs and functional domains.

An alignment was made of the deduced amino acid sequences of the entire capsid protein VP1 of all human rhinovirus (HRV) prototype strains to examine conserved motifs in the primary structure. A set of previously proposed crucially important amino acids in the footprints of the two known receptor molecules was not conserved in a receptor group-specific way. In contrast, VP1 and VP3 amino acids in the minor receptor-group strains corresponding to most of the predicted ICAM-1 footprint definitely differed from those of the ICAM-1-using major receptor-group strains. Previous antiviral-sensitivity classification showed an almost-complete agreement with the species classification and a fair correlation with amino acids aligning in the antiviral pocket. It was concluded that systematic alignment of sequences of related virus strains can be used to test hypotheses derived from molecular studies of individual model viruses and to generate ideas for future studies on virus structure and replication.

Capsid↗

PubMed2005

Environmental surveillance of wild poliovirus circulation in Egypt--balancing between detection sensitivity and workload.

Examination of sewage specimens for poliovirus (environmental surveillance) was adopted as a supplementary tool in the surveillance of poliomyelitis in Egypt. Sewage samples were concentrated about 50-fold using a simple two-phase separation technique, and inoculated in cell cultures in two collaborating laboratories in parallel. All but 9 of the 293 (97%) samples collected from January 2001 to December 2002 contained poliovirus and/or other enteroviruses, with polioviruses being detected in 84% of the samples. The proportion of specimens containing type 1 wild poliovirus (PV1W, the North-East African (NEAF) genotype) was less in 2002 (16%) than in 2001 (57%), and further decreased in 2003. While the overall sensitivity to detect PV1W was similar in the two collaborating laboratories, the specimens scored positive were not identical. Parallel cultures inoculated with aliquots of a given specimen very frequently resulted in isolation of different viruses. Moreover, partial sequence analysis occasionally revealed representatives of different genetic lineages of PV1W in a given specimen. These results emphasize the need to use intensive laboratory analysis to optimise sample sensitivity in environmental poliovirus surveillance, and the difficulties in reproducing the isolation results by simple re-inoculation of samples containing a mixture of different viruses.

Animals↗

PubMed2005

Phylogenetic analysis of human rhinovirus capsid protein VP1 and 2A protease coding sequences confirms shared genus-like relationships with human enteroviruses.

Phylogenetic analysis of the capsid protein VP1 coding sequences of all 101 human rhinovirus (HRV) prototype strains revealed two major genetic clusters, similar to that of the previously reported VP4/VP2 coding sequences, representing the established two species, Human rhinovirus A (HRV-A) and Human rhinovirus B (HRV-B). Pairwise nucleotide identities varied from 61 to 98 % within and from 46 to 55 % between the two HRV species. Interserotypic sequence identities in both HRV species were more variable than those within any Human enterovirus (HEV) species in the same family. This means that unequivocal serotype identification by VP1 sequence analysis used for HEV strains may not always be possible for HRV isolates. On the other hand, a comprehensive insight into the relationships between VP1 and partial 2A sequences of HRV and HEV revealed a genus-like situation. Distribution of pairwise nucleotide identity values between these genera varied from 41 to 54 % in the VP1 coding region, similar to those between heterologous members of the two HRV species. Alignment of the deduced amino acid sequences revealed more fully conserved amino acid residues between HRV-B and polioviruses than between the two HRV species. In phylogenetic trees, where all HRVs and representatives from all HEV species were included, the two HRV species did not cluster together but behaved like members of the same genus as the HEVs. In conclusion, from a phylogenetic point of view, there are no good reasons to keep these two human picornavirus genera taxonomically separated.

Cysteine Endopeptidases↗

PubMed2004

Presence of specific viruses in the middle ear fluids and respiratory secretions of young children with acute otitis media.

The purpose of the study was to investigate the presence of different viruses in middle ear fluids and nasopharyngeal aspirates in young children with acute otitis media. Two cohorts of children (N = 329 and 611) were followed from 2 to 24 months of age in Finland in two prospective studies (Finnish Otitis Media Cohort Study and Finnish Otitis Media Vaccine Trial). During the study period, nasopharyngeal and middle ear fluid specimens for each acute otitis media event were examined for eight (Cohort Study) or ten (Vaccine Trial) common respiratory viruses; adenoviruses, influenza viruses A and B, parainfluenza viruses 1, 2, and 3, respiratory syncytial virus (RSV), enteroviruses, parechoviruses, and rhinoviruses. Picornaviruses (rhinoviruses, enteroviruses, and parechoviruses) were determined by reverse transcription PCR while antigen detection was used for the other viruses. A virus was present in either nasopharyngeal or middle ear specimen in 54% of events in the first cohort and in 67% of events in the second. Rhinoviruses formed the most common virus group detected (41-32%), followed by enteroviruses (25%, sought in the second cohort only) and respiratory syncytial virus (RSV) (10%). All the other viruses represented jointly 8-10% of the events. In conclusion, using the methods described in this study, a specific virus infection was diagnosed in two thirds of all acute otitis media events in young children. Picornavirus RNA was detected in association with more than a half of all acute otitis media events. The use of PCR-based methods for the other respiratory viruses might have increased further the overall virus detection rate in acute otitis media.

Acute Disease↗

PubMed2004

Characterization of a highly evolved vaccine-derived poliovirus type 3 isolated from sewage in Estonia.

Two types of vaccine-derived polioviruses have been recently designated to emphasize the different origins of the evolved viruses: circulating vaccine-derived polioviruses (cVDPV) associated with outbreaks of paralytic disease and strains isolated from chronically infected immunodeficient individuals (iVDPV). We describe here a type 3 VDPV (PV3/EST/02/E252; later E252) isolated from sewage collected in Tallinn, Estonia, in October 2002. Due to aberrant properties in subtyping, the virus was subjected to detailed characterization. Partial genomic sequencing suggested that the closest relative was the oral vaccine strain PV3/Sabin, but the two virus strains shared only 86.7% of the 900 nucleotides (nt) coding for the capsid protein VP1. Phylogenetic analysis of the nearly complete genome [nt 19 to poly(A)] revealed multiple nucleotide substitutions throughout the genome and a possible Sabin 3/Sabin 1-recombination junction site in the 2C coding region. A calculation based on the estimated mutation frequency of the P1 region of polioviruses suggested that the E252 virus might have replicated in one or more individuals for approximately 10 years. No persons chronically excreting poliovirus are known in Estonia. Amino acid substitutions were seen in all known antigenic sites, which was consistent with the observed aberrant antigenic properties of the virus demonstrated by both monoclonal antibodies and human sera from vaccinated children. In spite of the apparent transmission potential, no evidence was obtained for circulation of the virus in the Estonian population.

Amino Acid Sequence↗

PubMed2003

Prolonged detection of indigenous wild polioviruses in sewage from communities in Egypt.

Environmental surveillance for polioviruses has been implemented in Egypt. This paper reports on a study in which 130 sewage samples were collected between January 2001 and December 2001 from eight provinces of Egypt. Samples were analyzed by virus isolation in L20B and RD cell cultures, and wild polioviruses were characterized by sequencing of the VP1 protein coding region. Wild type 1 polioviruses were detected in 57% of the sewage samples and 91% of the study sites, only two of which reported paralytic poliomyelitis cases in 2001. Three genetic lineages of a single indigenous type 1 poliovirus genotype were detectable in sewage, and only one lineage was also detected through surveillance for acute flaccid paralysis. Wild polioviruses persisted in the environment despite implementation of oral poliovirus vaccine immunization campaigns. Continued analysis of sewage samples, critical evaluation of immunization coverage, and performance of surveillance for acute flaccid paralysis are proposed as follow-up activities.

Adolescent↗

PubMed2003

Human rhinoviruses.

Human rhinoviruses are the most important causative agents of upper respiratory infections and are also implicated in more severe clinical entities. Although often present, very little is known about human rhinoviruses. Molecular methods have been used in the classification of this large group of viruses into two separate clades. In addition, one known serotype was found to be a member of enterovirus group D. Laboratory diagnosis of human rhinovirus infection is based on reverse transcription polymerase chain reaction methods or the more tedious virus culture but a rapid "bedside" method is unavailable. Anti-rhinoviral therapy has been under extensive study over the past few decades but symptomatic treatment of the common cold is still the only useful approach in clinical use. More data on circulating human rhinovirus strains would facilitate both detection and treatment of these common pathogens.

Acute Disease↗

PubMed2003

Characterization of a recombinant type 3/type 2 poliovirus isolated from a healthy vaccinee and containing a chimeric capsid protein VP1.

A Sabin 3/Sabin 2/Sabin 3 (S3/2/3) intertypic recombinant poliovirus was isolated from a faecal specimen from a 2-year-old healthy boy approximately 12 weeks after administration of oral poliovirus vaccine. The first recombination junction was in the genomic region encoding the VP1 capsid protein between nucleotide positions 3274 and 3285 (numbering according to Sabin 3) and the second was in the RNA polymerase region (nucleotide positions 6824 and 6825). The recombination had introduced six Sabin 2-derived amino acids into the Sabin 3 capsid environment in the carboxyl terminus of VP1. The complete genome of the recombinant virus differed from corresponding parental Sabin strains at 33 nucleotide positions, nine of them resulting in an amino acid substitution. Four substitutions were in the capsid proteins and five were in the region encoding the non-structural proteins. One amino acid was changed in the antigenic site 2B and two in site 3B. In addition, the whole antigenic site 3A was replaced by Sabin 2-specific amino acids, but the antigenic characteristics of the S3/2/3 did not show type 2-specific features. Neutralizing antibody titres in sera from Finnish children immunized with the inactivated poliovirus vaccine were not lower against the recombinant virus than against Sabin 3. Our results suggest that the chimeric virus was most likely generated by recombination events in the vaccinee, rather than representing progeny of circulating vaccine-derived virus.

Amino Acid Substitution↗

PubMed2003

Sequence and structure of human rhinoviruses reveal the basis of receptor discrimination.

The sequences of the capsid protein VP1 of all minor receptor group human rhinoviruses were determined. A phylogenetic analysis revealed that minor group HRVs were not more related to each other than to the nine major group HRVs whose sequences are known. Examination of the surface exposed amino acid residues of HRV1A and HRV2, whose X-ray structures are available, and that of three-dimensional models computed for the remaining eight minor group HRVs indicated a pattern of positively charged residues within the region, which, in HRV2, was shown to be the binding site of the very-low-density lipoprotein (VLDL) receptor. A lysine in the HI loop of VP1 (K224 in HRV2) is strictly conserved within the minor group. It lies in the middle of the footprint of a single repeat of the VLDL receptor on HRV2. Major group virus serotypes exhibit mostly negative charges at the corresponding positions and do not bind the negatively charged VLDL receptor, presumably because of charge repulsion.

Amino Acid Sequence↗

PubMed2002

Viral etiology of frequently recurring respiratory tract infections in children.

The viral etiology of frequently recurring respiratory tract infection (FRRI) in children aged <2 years was studied. Altogether, 329 children were followed from 2 to 24 months of age in the Finnish Otitis Media Cohort Study. Children with FRRI were defined as having > or =9 episodes of upper respiratory tract infection (URI) and/or > or =4 episodes of acute otitis media during follow-up. Nasopharyngeal aspirates, middle ear fluid specimens, and serum samples were analyzed for 8 common respiratory viruses. Of 1358 URI episodes, 642 (47%) occurred in the 78 children with FRRI. At least 1 virus was associated with 62% of these episodes, whereas the corresponding figure for children without FRRIs was 54%. The frequency of different viruses was similar in both groups, but the relative proportion of rhinovirus infections was slightly higher among children with FRRI. In conclusion, a specific viral etiology does not explain the excess of URI episodes in children with FRRI.

Child, Preschool↗

PubMed2002

Genetic clustering of all 102 human rhinovirus prototype strains: serotype 87 is close to human enterovirus 70.

Human rhinoviruses (HRV), common agents of respiratory infections, comprise 102 designated serotypes. The genetic relationships of HRV prototype strains and the possibility of using genetic identification of a given HRV field strain were studied. Genomic sequences in the VP4/VP2 region were obtained from all 102 prototype strains. Phylogenetic analysis included 61 recently isolated Finnish field strains. Seventy-six out of the 102 prototype strains clustered in the HRV genetic group A and 25 in group B. Serotype 87 clustered separately and together with human enterovirus 70. The 'percentage' interserotypic differences were generally similar to those between different enterovirus serotypes, but for six pairs of HRV serotypes they were less than 10%. The maximum variation in genetic group A was 41% at the nucleotide level and 28% at the amino acid level, and in genetic group B 34% and 20%, respectively. Judging from the observed interserotypic differences, the 61 Finnish field isolates might represent as many as 19 different serotypes. One cluster of the field strains did not directly associate with any of the prototype strains and might represent a new serotype. However, larger numbers of field isolates of known serotype need to be characterized, possibly also in the VP1 region, to evaluate the feasibility of genetic typing of HRV strains.

Capsid↗

PubMed2002

Human rhinovirus 87 and enterovirus 68 represent a unique serotype with rhinovirus and enterovirus features.

It has recently been reported that all but one of the 102 known serotypes of the genus Rhinovirus segregate into two genetic clusters (C. Savolainen, S. Blomqvist, M. N. Mulders, and T. Hovi, J. Gen. Virol. 83:333-340, 2002). The only exception is human rhinovirus 87 (HRV87). Here we demonstrate that HRV87 is genetically and antigenically highly similar to enterovirus 68 (EV68) and is related to EV70, the other member of human enterovirus group D. The partial nucleotide sequences of the 5' untranslated region, capsid regions VP4/VP2 and VP1, and the 3D RNA polymerase gene of the HRV87 prototype strain F02-3607 Corn showed 97.3, 97.8, 95.2, and 95.9% identity to the corresponding regions of EV68 prototype strain Fermon. The amino acid identities were 100 and 98.1% for the products of the two capsid regions and 97.9% for 3D RNA polymerase. Antigenic cross-reaction between HRV87 and EV68 was indicated by microneutralization with monotypic antisera. Phylogenetic analysis showed definite clustering of HRV87 and EV68 with EV70 for all sequences examined. Both HRV87 and EV68 were shown to be acid sensitive by two different assays, while EV70 was acid resistant, which is typical of enteroviruses. The cytopathic effect induced by HRV87 or EV68 was inhibited by monoclonal antibodies to the decay-accelerating factor known to be the receptor of EV70. We conclude that HRV87 and EV68 are strains of the same picornavirus serotype presenting features of both rhinoviruses and enteroviruses.

Amino Acid Sequence↗