Genetic diversity and rapid evolution of poliovirus in human hosts.
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Biological Evolution↗
Biomedical subjects
L Kinnunen
Publications and source records attributed to L Kinnunen.
Evolution of influenza B/Victoria/2/87-like viruses: occurrence of a genetically conserved virus under conditions of low epidemic activity.
Nucleotide sequence analysis of the gene region coding for the HA1 domain of the influenza B virus haemagglutinin was performed on seven field strains isolated during the 1989 to 1990 season and two field strains isolated in 1985 and 1988 in Finland. All isolates were antigenically and genetically related to B/Victoria/2/87 virus and distinct from B/Yamagata/16/88 virus. The three strains isolated at the beginning of the 1989 1990 season in Turku were almost identical to an American variant (B/Texas/37/88-B/Ohio/10/88) of the previous season, whereas the four strains isolated later in the 1989 to 1990 season in Helsinki formed a new group of heterogeneous viruses. The phylogenetic tree compiled suggests that the two branches had evolved from a common origin, probably in 1987.
Amino Acid Sequence↗
Genetic variation in vivo and proposed functional domains of the 5' noncoding region of poliovirus RNA.
Poliovirus has a single-stranded RNA genome of about 7,440 nucleotides (nt) with an unusually long 750-nt noncoding region in the 5' end (5'NCR). Several regulatory functions have been assigned to the 5'NCR. We sequenced the 5'NCRs of 33 wild-type 3 poliovirus strains to study the range and distribution of naturally occurring sequence variations. In this regard, the 5'NCR can be divided into a conserved part (nt 1 to 650) and a hypervariable part (nt 651 to 750). In the conserved part, altogether 234 unevenly distributed nucleotide positions (36%) showed variation. When these positions were plotted against the predicted secondary-structure models, it was found that the existence of most of the proposed stem-loop structures was supported by extensive structure-conserving substitutions in the stems. Regions with conserved sequences, as well as mutational hot spots, were observed. The hypervariable part of the 5'NCR varied up to 56% between the strains studied. The A + U percentage was significantly higher than in the conserved part. The number of AUG codons varied between 5 and 15 in the conserved part of the 5'NCR, while none was found in the hypervariable part. These results provide information that can be used in site-directed mutagenesis and other approaches targeted to reveal the functional domains of the 5'NCR.
Base Sequence↗
Generation of virus genetic lineages during an outbreak of poliomyelitis.
Wild poliovirus type 3 isolates collected during the Finnish outbreak (1984 to 1985) in different geographical locations were compared by partial RNA sequencing. The entire 5' non-coding end and a discontinuous part of the capsid coding region were sequenced from 15 isolates. Combining the present sequence data with previously published data and analysing these by the maximum parsimony method showed that the epidemic strains had diverged in cocirculating lineages. Genetic comparison of strains isolated from a single person often revealed a branched structure in the phylogenetic tree indicating high potential for diversification. The extent of variation generated under immunological pressure during an infection lasting for weeks in one person was high as compared with the observed geographical variation.
Antigens, Viral↗
Genomic variation of herpes simplex virus type 2 isolates analysed by hybridization after electroblotting from polyacrylamide gels.
Genomic variation of herpes simplex virus type 2 (HSV-2) strains was analysed by polyacrylamide gradient gel electrophoresis and subsequent hybridization to cloned HSV-2 sequences. Two probes were used, one from the L-segment and one from the S-segment of the HSV-2 genome. The probes did not contain a-repeat sequences. Hybridization to the specific sequences in individual DNA fragments obtained by use of the frequently cleaving restriction endonuclease Alu I revealed variations in the genome not detectable by analysing the fragment size only. The use of 35S-labelled deoxynucleotide in the radioactive labelling of the probe further improved the resolution of the method.
DNA, Viral↗
Type 3 poliovirus/Finland/1984 is genetically related to common Mediterranean strains.
Strains of poliovirus type 3 isolated in Finland in 1984 and 1985 (P3/Fin/84) are known to differ considerably from the type 3 vaccine strains in both nucleotide sequence and antigenic properties. In the search for the origin of the outbreak we first tested 80 type 3 strains that had been isolated elsewhere in the world during the years 1953 to 1986. An oligonucleotide probe complementary to a highly variable 17 nucleotide interval in the 5' non-coding region of the genomic RNA of P3/Fin/84 reacted with five strains. Also it was revealed that two of the latter five strains were related to the P3/Fin/84 strains in two separate genomic regions compared after partial RNA sequencing. One of them was isolated in Switzerland in 1980 and the other in Turkey in 1981. The Swiss strain was from a patient who had recently returned from a journey to various Mediterranean countries. Consequently, 16 other strains isolated in the late 1970s and early 1980s in Europe or in the Mediterranean countries were studied in detail by partial genomic sequencing and with neutralizing monoclonal antibodies. Two separate regions of the genome were compared by sequencing and corresponding dendrograms were constructed. The Switzerland and Turkey strains were found to be the strains most closely related to the viruses of the 1984 Finland epidemic. These results indicate that type 3 poliovirus strains related to P3/Fin/84 had been circulating in Mediterranean countries since the late 1970s.
Amino Acid Sequence↗
Rapid molecular evolution of wild type 3 poliovirus during infection in individual hosts.
A panel of nine neutralizing monoclonal antibodies was used to analyse the antigenic properties of 188 plaque-purified type 3 poliovirus strains from 17 faecal specimens, derived from eight people during a 2 month observation period. Most poliovirus specimens consisted of a mixture of antigenically distinct variants and the composition of the mixture was found to change between sequential specimens in many individuals, indicating antigenic evolution. Thirty-five strains representing different antigenic patterns were selected for partial sequencing of genomic RNA. Mutations leading to amino acid substitutions, as well as silent mutations, were seen at and close to the known antigenic sites. The frequency of silent mutations was used to estimate the evolutionary potential of the virus. The largest difference in silent changes between strains isolated from one person was 0.8%, which corresponds to a minimum of about 60 mutations per genome within a period of 3 weeks. The observed incidence of silent mutations between isolates from different persons was usually between 0.8 and 2%. These figures agree with the previously reported overall mutation rates of poliovirus, determined by other methods.
Amino Acid Sequence↗
Partial RNA sequencing of eight supposed derivatives of type 3 poliovirus/USA/Saukett/50 reveals remarkable differences between three apparent substrains.
Eight supposed derivatives of type 3 poliovirus/USA/Saukett/50 could be divided in three subgroups differing from each other as much as from the independent P3/Sabin strain as judged by partial genomic sequences covering about 25% of the portion of RNA coding for the structural proteins. This suggests that strains designated as Saukett in different laboratories are derived from three separate but related American isolates of type 3 poliovirus. Deduced amino acid sequence of the "Saukett" strains revealed amino acid substitutions at all known major antigenic sites compared with P3/Sabin or P3/Finland/23127/84 strain, but also between individual Saukett strains. These substitutions may be responsible for the known antigenic differences between the studied strains.
Amino Acid Sequence↗
Poliovaccine virus in the cerebrospinal fluid after oral polio vaccination.
In February-March 1985 an oral poliovirus vaccine campaign was launched in Finland in a population vaccinated earlier with inactivated poliovaccine. During this campaign a strain of poliovirus was isolated from the cerebrospinal fluid (CSF) of a 7-year-old girl 34 days after she had received oral poliovirus vaccine. She had long-lasting headache, vomiting and fever but no paralysis. This case demonstrates that poliovaccine virus can invade the central nervous system even after a complete course of inactivated poliovirus vaccine if the inactivated vaccine has been poorly antigenic against one of the three types of virus.
Cerebrospinal Fluid↗
Restricted variability of a 17 nucleotide stretch within the 5'-noncoding region of poliovirus genome.
The outbreak of poliomyelitis in Finland in 1984 was caused by a wild strain of poliovirus 3 with uncommon molecular and antigenic properties. We prepared a synthetic oligonucleotide probe complementary to nucleotides 494-510 in the 5'-noncoding part of the genome of a representative strain of the outbreak. This short nucleotide stretch was found to be relatively well conserved within the outbreak and uncommon among 82 independent poliovirus isolates. It may thus be a useful marker for screening isolates to identify those requiring more detailed genetic comparison. The sequences of the corresponding region of the genome are known for 32 separate poliovirus strains and 3 coxsackie B virus strains and show 6 fully conserved nucleotides that could assume a constant hairpin-loop position in a hypothetical secondary structure of the RNA. This could explain the persistence of a particular 17 nucleotide sequence for 40 years in nature in this highly variable region of the poliovirus genome.
Animals↗
Antigenic variation among 173 strains of type 3 poliovirus isolated in Finland during the 1984 to 1985 outbreak.
Antigenic properties of 128 clinical type 3 poliovirus isolates of the 1984 to 1985 Finland outbreak from 95 persons and 45 strains from sewage water specimens were evaluated using five neutralizing monoclonal antibodies (MAbs) directed against an antigenic site (designated site 1) on VP1 at amino acids 89 to 100. All five MAbs neutralized the type 3 poliovirus strains used in the vaccines, P3/Saukett and P3/Sabin, but none of them neutralized the prototype strain of the outbreak (P3/Finland/23127/84). Forty-six percent of the clinical isolates resembled the prototype strain (class A) while the rest of the isolates were neutralized by one or more of the MAbs (classes B to D). Although an antigenic drift from A to one of the other classes was observed in sequential specimens from several individuals, no clear-cut overall change in the class distribution was found within the 3 months time span of the outbreak. Homogeneous virus populations were isolated from the sewage specimens using a microtitre endpoint dilution method. The last positive sewage specimens which were obtained in January to February 1985 still had a majority of the class A strain. Some of the clinical isolates were also tested using MAbs directed against distinct antigenic sites. These studies showed that strains that gave the same pattern of reactivity with site 1 MAbs could be differentiated using antibodies directed against other sites. Fifteen strains belonging to different antigenic subclasses were subjected to partial RNA sequencing of the genome region coding for antigenic site 1. The antigenic variation was usually, but not always associated with corresponding amino acid substitutions in antigenic site 1. These results indicate that the antigenic sites of type 3 poliovirus vary extensively within a given outbreak and even during replication in a given host. This variation may have both pathogenetic and epidemiological significance.
Amino Acid Sequence↗
Improved sensitivity of restriction endonuclease analysis of herpes simplex virus type 2 DNA with polyacrylamide gradient gel electrophoresis.
Polyacrylamide gradient gel electrophoresis was used to resolve fragments of herpes simplex virus type 2 (HSV-2) DNA, produced by the restriction endonucleases Alu I, Bam HI, Pst I, and Sma I, which cleave the HSV-2 DNA into more than 30 fragments each. HSV-2 strains isolated from different individual patients could be easily distinguished from each other by the endonucleases Bam HI and Sma I. Successive virus isolates from a single person, analyzed using Alu I and Sma I, showed variability of fragment patterns. The effect of passaging the virus in cell cultures for several cycles was evaluated with the restriction endonuclease Alu I. No differences were found after 29 successive passages in VERO cells. Polyacrylamide gradient gel analysis of restriction endonuclease digests of HSV-2 DNA enables the use of enzymes that cleave the DNA into a great number of fragments, thus improving the sensitivity of analysis.
Animals↗
Evolution of poliovirus during an outbreak: sequential type 3 poliovirus isolates from several persons show shifts of neutralization determinants.
An outbreak of poliomyelitis in Finland resulted in the widespread circulation of wild-type 3 poliovirus strains that had antigenic properties distinct from the strains used to produce the attenuated and inactivated vaccines. Considerable variation was observed in the ability of broadly reacting monoclonal antibodies directed against type 3 poliovirus to neutralize the 54 strains examined. Sequential isolates from several persons showed an antigenic drift with these monoclonal antibodies and selected human sera. In addition, some faecal specimens were found to contain more than one antigenic variant. Primer extension sequencing of genomic RNAs of three plaque-purified antigenic variants isolated from one patient showed base substitutions in the region coding for the major antigenic site of poliovirus type 3. The resulting difference in the amino acid sequence in the virion protein VP1 could explain the differences observed in the neutralization of these strains by the monoclonal antibodies. Whether the observed changes in the antigenic characteristics of the sequential isolates represent true antigenic drift under immunological pressure or whether the emergence of the new variants is based on other modes of selection during replication is not known.
Antibodies, Monoclonal↗
Serum immunoglobulin levels in the course of bacterial meningitis in children.
Serum levels of 5 immunoglobulins (IgG, IgA, IgM, IgD and IgE) were determined at frequent intervals in the course of bacterial meningitis in children. 59 patients were examined; 27 with Haemophilus influenzae meningitis, 23 with meningococcal and 9 with pneumococcal meningitis. All 5 immunoglobulins increased during the 2-week course of bacterial meningitis. IgM was the immunoglobulin class responding most rapidly, regularly and intensively. IgG increased moderately. However, practically no rise of the IgG level was observed in children with H. influenzae meningitis. The elevation of the IgA and IgE levels possibly suggests that meningitis may also cause synthesis of IgA and IgE antibodies. The results of the study indicate that antibodies of all the 5 immunoglobulin classes are probably involved in the defense against the causative microbes in bacterial meningitis.
Bacterial Infections↗
Evolution of influenza A(H1N1) viruses during a period of low antigenic drift in 1986-91: sequence of the HA1 domain of influenza A/Finland/158/91.
This study used the nucleotide sequence coding for the HA1 domain of virus haemagglutinin to show that influenza A/Finland/158/91, which represents the H1N1 subtype viruses prevalent in Finland in 1990/91, was a direct descendant of a virus (A/NN/1605/88) isolated during the 1988/89 epidemic season in Japan. The elevated rate of 7.4 x 10(-3) nucleotide substitutions per site per year is discussed. The new branch of H1N1 subtype viruses is characterized by loss of a glycosylation site, which may affect subsequent antigenic drift.
Amino Acid Sequence↗