Evolution of the G and P genes of human respiratory syncytial virus (subgroup A) studied by the RNase A mismatch cleavage method

Antigenic and genetic variability of human respiratory syncytial viruses (group A) isolated in Uruguay and Argentina: 1993-2001

The antigenic and genetic diversity of G glycoprotein from 25 human respiratory viruses (group A) isolated during nine consecutive epidemics (1993-2001) in Montevideo, Uruguay, and 7 strains isolated in Buenos Aires, Argentina, in the same period were analyzed. Genetic variability was evaluated by partial sequence of the G protein gene. Phylogenetic analysis indicated that most Uruguayan and Argentinean group A isolates clustered into three genotypes: GA5, GA2, and GA1. Some strains clustered into the GA3 genotype characterized previously. The antigenic analysis was carried out with a panel of anti-G monoclonal antibodies that recognized conserved and strain-specific epitopes. A close correlation between the antigenic and genetic relatedness of the strains analyzed was observed.

Genetic variability of respiratory syncytial virus subgroup a strain in 15 successive epidemics in one city

The genetic variability of 125 respiratory syncytial virus (RSV) subgroup A isolates over 15 successive epidemics from 1980 to 1995 in an urban population of Japan was determined. Allocation of isolates into lineages was archived by reverse transcriptase-polymerase chain reaction amplification of selected regions of the nucleoprotein (NP) and attachment (G) protein gene followed by restriction fragment length polymorphism (RFLP) analysis. Three and seven distinct restriction patterns of the NP and G gene were observed, respectively. When the NP and G gene RFLP analyses were combined, ten different genetic lineages were identified in the 125 isolates. The strains with the same genotype were isolated in each epidemic and the dominant lineages were replaced by others after every one to three consecutive epidemics. Nucleotide and amino acid sequencing of the variable region of G gene of these predominant isolates revealed differences of 5--28% between strains. There was, however, no apparent accumulation of diversity with age to indicate progressive changes. The dominant strains were often closely related to those isolated in other parts of the world at a similar time. These observations suggest that dominant RSV strains are replaced frequently by others that have been co-circulating or have recently entered the community from a worldwide reservoir. The change of dominant strains may be influenced by the buildup of immunological resistance in the community to successive epidemics of the same strain.

Molecular epidemiology of respiratory syncytial virus

Human respiratory syncytial virus (RSV) is the major cause of lower respiratory tract disease in infants. It is unusual in that it causes repeated infections throughout life. Despite considerable efforts there is as yet no satisfactory vaccine available. This paper reviews the molecular epidemiology of the RSV and describes the complex genotypic structure of RSV epidemics. The evolution of the virus is discussed, with particular reference to the antigenic and genetic variability of the attachment glycoprotein.

Respiratory syncytial virus: changes in prevalence of subgroups A and B among Argentinian children, 1990-1996

The frequency of respiratory syncytial virus (RSV) and the distribution of subgroups A and B strains during 7 consecutive years (1990-1996) were examined in two cities of Argentina. Nasopharyngeal aspirates from 1,304 children less than 2 years of age hospitalized with acute lower respiratory infection were studied by indirect immunofluorescence. RSV was detected in 352 cases (26.9%), and the peak activity was observed in midwinter. Subgroup characterization was performed with two monoclonal antibodies against the F protein on nasopharyngeal aspirate smears. Of 195 samples, 174 (89.2%) were identified as subgroup A strains and 21 (10.8%) as subgroup B. Both strains cocirculated during 5 of 7 years studied with subgroup A predominating. Subgroup A occurred at least 8 times as often in all years except for 1994-1995. Children infected by subgroup A were younger than those infected by subgroup B (P < 0.05). The association of subgroup A infection with bronchiolitis and subgroup B with pneumonia was statistically significant (P < 0.03).

Respiratory syncytial virus genetic and antigenic diversity

Respiratory syncytial virus (RSV) is a major cause of viral lower respiratory tract infections among infants and young children in both developing and developed countries. There are two major antigenic groups of RSV, A and B, and additional antigenic variability occurs within the groups. The most extensive antigenic and genetic diversity is found in the attachment glycoprotein, G. During individual epidemic periods, viruses of both antigenic groups may cocirculate or viruses of one group may predominate. When there are consecutive annual epidemics in which the same group predominates, the dominant viruses are genetically different from year to year. The antigenic differences that occur among these viruses may contribute to the ability of RSV to establish reinfections throughout life. The differences between the two groups have led to vaccine development strategies that should provide protection against both antigenic groups. The ability to discern intergroup and intragroup differences has increased the power of epidemiologic investigations of RSV. Future studies should expand our understanding of the molecular evolution of RSV and continue to contribute to the process of vaccine development.

Respiratory syncytial virus genetic and antigenic diversity

Respiratory syncytial virus (RSV) is a major cause of viral lower respiratory tract infections among infants and young children in both developing and developed countries. There are two major antigenic groups of RSV, A and B, and additional antigenic variability occurs within the groups. The most extensive antigenic and genetic diversity is found in the attachment glycoprotein, G. During individual epidemic periods, viruses of both antigenic groups may cocirculate or viruses of one group may predominate. When there are consecutive annual epidemics in which the same group predominates, the dominant viruses are genetically different from year to year. The antigenic differences that occur among these viruses may contribute to the ability of RSV to establish reinfections throughout life. The differences between the two groups have led to vaccine development strategies that should provide protection against both antigenic groups. The ability to discern intergroup and intragroup differences has increased the power of epidemiologic investigations of RSV. Future studies should expand our understanding of the molecular evolution of RSV and continue to contribute to the process of vaccine development.

Genetic analysis of the G and P genes in ungulate respiratory syncytial viruses by RNase A mismatch cleavage method

The G and P genes of bovine, ovine and caprine respiratory syncytial (RS) viruses were analyzed by RNase A one-dimensional fingerprinting, using A 51908 as the reference strain. Antisense G or P RNA probes of bovine RS virus strain A 51908 were hybridized to total RNA extracted from bovine turbinate cells infected with bovine, ovine or caprine RS virus strains. The RNA:RNA heteroduplexes were digested with RNase A and the resistant products were analyzed by gel electrophoresis. Comparative analysis of the cleavage patterns revealed heterogeneity among bovine, ovine and caprine RS virus isolates. Ovine RS virus strains generated RNA cleavage patterns more distantly related to the bovine or caprine RS virus strains, particularly in the G gene. Statistical analysis of the results obtained indicated that genetic differences between bovine and ovine viruses were larger, compared with the ones among bovine strains themselves. The same analysis also revealed a close genetic relation among bovine and caprine strains. These results are discussed in terms of ungulate RS virus genetic variation and vaccine development.

Experimental evaluation of the ribonuclease protection assay method for the assessment of genetic heterogeneity in populations of RNA viruses

The ribonuclease (RNase) protection assay (RPA) was evaluated as a method to estimate genetic distances among sequence variants of RNA viruses. The patterns of fragments generated, under different RPA conditions, by three sets of RNA sequence variants of known nucleotide sequence, were analyzed. Both the effectiveness of cleavage (i.e. the probability of cleavage in a certain heteroduplex) and its degree (i.e. in all the molecules in the assay or in a part of them) varied largely according to the nature of the mismatch. Probability and degree of cleavage were also dependent on distant sequence context effects. No correlation could be established between context and cleavage, so that the pattern of fragments in RPA cannot be unequivocally predicted from sequence information. Accordingly, nucleotide sequence differences between two sequence variants cannot be directly derived from RPA data. For all three sequence sets linear relationships were found between the number of non-shared fragments in the RPAs of two variants and their nucleotide sequence differences. Nevertheless, both linearity and the linear regression parameters varied largely according to the sequence set and according to RPA conditions, in a non-predictable way. Thus, under experimental conditions, RPA may not be as appropriate a method to estimate genetic distances between RNA sequences as simulation under an ideal model suggested. Possible ways to diminish the gap between the ideal model and the experimental procedure are proposed.

Molecular epidemiology of respiratory syncytial virus: a review of the use of reverse transcription-polymerase chain reaction in the analysis of genetic variability

Respiratory syncytial virus (RSV) is the major viral cause of lower respiratory tract disease (bronchiolitis and pneumonia) in babies and infants. Infections with the virus occur as annual winter epidemics in temperate climates, placing considerable pressure on the provision of hospital beds. The virus is unusual in that it can reinfect individuals and it can infect babies despite the presence of maternal antibody. RSV has a negative sense nonsegmented RNA genome and as such is liable to high levels of mutation. This paper describes methods developed to determine the degree of genetic variability of the virus both during individual epidemics and worldwide. It is necessary for these methods to be quick, easy and cheap so that large numbers of samples can be analysed readily. They are based on extraction of viral RNA directly from clinical samples or from viral cultures, reverse transcription of the viral RNA, and then amplification of selected regions of the genome by the polymerase chain reaction (PCR). PCR products are then analysed by restriction mapping, or, if necessary, direct nucleotide sequencing. In this way isolates of RSV have been shown to fall into a number of genotypes, with epidemics being made up of cocirculating genotypes whose relative proportions vary with each epidemic. An understanding of the molecular epidemiology of this important human pathogen will be of significance in the search for an effective vaccine.

Comparative study of the genetic variability in thymidine kinase and glycoprotein B genes of herpes simplex viruses by the RNase A mismatch cleavage method

The variability of herpes simplex viruses has been measured using the RNAse A mismatch cleavage method in two genes: thymidine kinase and glycoprotein B of both HSV-1 and HSV-2. This technique permitted us to study the variability of the virus with a greater level of resolution than restriction endonuclease analysis. The phylogenetic trees obtained for the different genes allowed us to identify consistent clusters of viruses circulating in the same geographical area. Our results showed that thymidine kinase is more heterogeneous than glycoprotein B for both subtypes of HSV, and confirmed that HSV-1 is more heterogeneous than HSV-2 for both genes. This is the first time that this kind of analysis has been applied to DNA viruses.

Evolutionary pattern of human respiratory syncytial virus (subgroup A): cocirculating lineages and correlation of genetic and antigenic changes in the G glycoprotein

The genetic and antigenic variability of the G glycoproteins from 76 human respiratory syncytial (RS) viruses (subgroup A) isolated during six consecutive epidemics in either Montevideo, Uruguay, or Madrid, Spain, have been analyzed. Genetic diversity was evaluated for all viruses by the RNase A mismatch cleavage method and for selected strains by dideoxy sequencing. The sequences reported here were added to those published for six isolates from Birmingham, United Kingdom, and for two reference strains (A2 and Long), to derive a phylogenetic tree of subgroup A viruses that contained two main branches and several subbranches. During the same epidemic, viruses from different branches were isolated. In addition, closely related viruses were isolated in distant places and in different years. These results illustrate the capacity of the virus to spread worldwide, influencing its mode of evolution. The antigenic analysis of all isolates was carried out with a panel of anti-G monoclonal antibodies that recognized strain-specific (or variable) epitopes. A close correlation between genetic relatedness and antigenic relatedness in the G protein was observed. These results, together with an accumulation of amino acid changes in a major antigenic area of the G glycoprotein, suggest that immune selection may be a factor influencing the generation of RS virus diversity. The pattern of RS virus evolution is thus similar to that described for influenza type B viruses, expect that the level of genetic divergence among the G glycoproteins of RS virus isolates is the highest reported for an RNA virus gene product.

Etiology and severity of community acquired pneumonia in children from Uruguay: a 4-year study

The 4-year study (1987-1990) covered the major clinical-epidemiological characteristics of pneumonia in children as diagnosed at the emergency service of the Children's Hospital, as well as etiologies, and factors involved in the most severe cases. Etiology was determined in 47.7% of the 541 pneumonia cases, involving 283 pathogens of which 38.6% were viruses and 12.6% bacteria. Viral and mixed etiologies were more frequent in children under 12 months of age. Bacteria predominated in ages between 6 and 23 months. Among the viruses, respiratory syncytial virus predominated (66%). The bacterial pneumonias accounted for 12.2% of the recognized etiologies. The most important bacterial agents were S. pneumoniae (64%) and H. influenzae (19%). H. influenzae and mixed infections had a relevant participation during the 1988 season, pointing to annual variations in the relative participation of pathogens and its possible implication in severity of diseases. Correlation of severity and increased percentage of etiological diagnosis was assessed: patients with respiratory rates over 70 rpm, or pleural effusion and/or extensive pulmonary parenchyma compromise yielded higher positive laboratory results. Various individual and family risk factors were recognized when comparing pneumonia children with healthy controls.

Analysis of respiratory syncytial virus strain variation in successive epidemics in one city

The variability of respiratory syncytial virus isolates from five successive epidemics in an urban population was determined. A total of 187 isolates of respiratory syncytial virus from the southern part of Birmingham, United Kingdom, were classified into subgroups A and B and were then further assigned to genetic lineages. Allocation of isolates into lineages was achieved by reverse transcription of infected cell RNA and then PCR amplification of selected regions of the genome; PCR products were examined by restriction mapping or nucleotide sequencing of parts of the nucleoprotein gene, the small hydrophobic protein gene, and the attachment protein gene. Previous work has shown that estimations of genetic diversity by analysis of genes coding for proteins likely (attachment protein) and unlikely (nucleoprotein and small hydrophobic protein) to be under immune pressure gave concordant results. Six genetic lineages of subgroup A isolates have been defined by this procedure; these isolates differ by up to 20% in the amino acid sequences of their attachment proteins; likewise, subgroup B isolates can be divided into two categories by restriction mapping of parts of their nucleoprotein and attachment protein genes. The same genetic lineages appeared to be present worldwide during the same period. The analysis of isolates from successive epidemics showed that different lineages predominated in each epidemic and that not all lineages were present in every epidemic. Some lineages appeared to increase in numbers over several years and then decline, possibly indicating a buildup of resistance in the community to a particular genotype.

Estimates by computer simulation of genetic distances from comparisons of RNAse A mismatch cleavage patterns

The RNAse A mismatch cleavage method was used to analyze genomic variability in RNA and DNA systems. However, there is no method which relates the digestion patterns observed to the extent of genetic variation. Here we report computer simulations which provide a simple estimator of genetic distances from the comparison of RNAse A digestion patterns. The results show that the number of non-shared fragments is proportional to the number of mutations between each pair of sequences compared. This prediction is supported by the comparison of the RNAse A mismatch patterns and the nucleotide sequences of a set of influenza A (H3N2) hemagglutinin genes. The procedure allows a quantitative and reliable use of the RNAse A mismatch cleavage method.

RNA hybrid mismatch polymorphisms in Australian populations of turnip yellow mosaic tymovirus

In the Mt. Kosciusko alpine area of Australia there are three well-separated populations of Cardamine lilacina, an endemic sward-forming perennial brassica, and these are infected with turnip yellow mosaic tymovirus. The genetic variation in these viral populations has been assessed by an RNA hybrid mismatch polymorphism method. About 100 isolates were examined; the genomic RNA of each isolate was prepared from a shoot of a single wild C. lilacina plant. RNA hybrid mismatch polymorphisms (RHMPs) were assessed in six regions of the genomes using labelled negative-strand probes transcribed from selected portions of a cloned TYMV genome. The probed region at the 3' end of the genome showed little variation and over 95% of the isolates gave the same pattern. However, other parts of the genome, including the 5' non-coding region, were much more variable. There was no significant correlation between groupings based on the RHMP patterns, and the location from which the isolates were collected, nor with the symptom type or severity shown by their host plants. The patterns of variation suggested that all three populations of the virus are a single quasi-species; at most one tenth of the isolates gave similar RHMP patterns, those of the "master copy".

Geographical clusters of dengue virus type 2 isolates based on analysis of infected cell RNA by the chemical cleavage at mismatch method

Genetic variation in 12 strains of dengue virus type 2, isolated from several epidemic areas in different years, was studied by chemical cleavage at mismatched cytosine in DNA:RNA heteroduplexes. End-labelled cDNA probes derived from the E and NS2A genes of the New Guinea C strain were hybridized to total RNA extracted from cells infected by individual isolates. Following modification of mismatched cytosine by hydroxylamine and nucleic acid strand cleavage by piperidine, the resulting fragments of radiolabelled probe were analysed by electrophoresis and autoradiography. The patterns of bands generated corresponded to the geographical groupings of the isolates. Thus this method is suitable in epidemiological studies for rapidly surveying a large number of isolates for genetic variation in a particular gene of interest.

Analysis of relatedness of subgroup A respiratory syncytial viruses isolated worldwide

Respiratory syncytial virus strains (subgroup A) isolated from around the world during the period 1988-1991 were analysed to determine their relatedness. Analysis was by restriction mapping and nucleotide sequencing following amplification of selected regions of the virus genome by polymerase chain reaction (PCR). Twenty-three viruses of subgroup A isolated from cities in temperate regions of the Northern and Southern hemispheres and the tropics during the period 1988-1991 fell into distinct groupings closely related to four of the six lineages defined in analysis of recurrent epidemics within the same city (Birmingham, UK) during the same period. These observations confirm that multiple lineages of RS virus co-circulate locally, and show that very similar viruses are present simultaneously in widely separated countries.