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

Assessing dissimilarity of genes by comparing their RNAse A mismatch cleavage patterns

We propose a simple algorithm for estimating the number of nucleotide differences between a pair of RNA or DNA sequences through comparison of their RNAse A mismatch cleavage patterns. In the RNAse A mismatch cleavage technique two or more sample sequences are hybridized to the same RNA probe, the hybrids are partially digested with RNAse A, and the digestion products are compared on an electrophoretic gel. Here we provide an algorithm for converting the numbers of unique and matching electrophoretic bands into an estimate of the number of nucleotide differences between the sequences. Computer simulation indicates that the proposed method yields a robust estimate of the genetic distance despite stochastic errors and occasional violation of certain assumptions. Our study suggests that the method performs best when the distance between the sequences is < 15 differences. When the sequences under analysis are likely to have larger distances, we advise to substitute one long riboprobe with a set of shorter nonoverlapping probes. The new algorithm is applied to infer the proximity of several strains of pseudorabies virus.

Selection response in finite populations

Formulae were derived to predict genetic response under various selection schemes assuming an infinitesimal model. Account was taken of genetic drift, gametic (linkage) disequilibrium (Bulmer effect), inbreeding depression, common environmental variance, and both initial segregating variance within families (sigma AW02) and mutational (sigma M2) variance. The cumulative response to selection until generation t(CRt) can be approximated as [equation: see text] where Ne is the effective population size, sigma AW infinity 2 = Ne sigma M2 is the genetic variance within families at the steady state (or one-half the genic variance, which is unaffected by selection), and D is the inbreeding depression per unit of inbreeding. R0 is the selection response at generation 0 assuming preselection so that the linkage disequilibrium effect has stabilized. beta is the derivative of the logarithm of the asymptotic response with respect to the logarithm of the within-family genetic variance, i.e., their relative rate of change. R0 is the major determinant of the short term selection response, but sigma Me2 Ne and beta are also important for the long term. A selection method of high accuracy using family information gives a small Ne and will lead to a larger response in the short term and a smaller response in the long term, utilizing mutation less efficiently.

A strain-type clustering of potato virus Y based on the genetic distance between isolates calculated by RFLP analysis of the amplified coat protein gene

Potato virus Y (PVY) isolates have been classified into genetic strains by a host-independent criterion using a molecular typing method. The method used extracts from infected tissue, and included immunocapture-RT-PCR-RFLP analysis using 5 different restriction endonucleases (Dde I, Eco RV, Hinf I, Rsa I and Taq I). Genetic distances between the different PVY "restrictotypes" were calculated and used to define the PVY genetic strains. Three main clusters were found: PVYO, PVYN, and non-potato PVY (PVYNP), in good agreement with classical PVY strain definitions that combine different biological criteria. Our approach was incomparably quicker and more reliable and reproducible than biotyping. The potential of this approach for very quick, simple and automatable molecular epidemiological studies is discussed.

A method for determining the position and size of optimal sequence regions for phylogenetic analysis

The availability of fast and accurate sequencing procedures along with the use of PCR has led to a proliferation of studies of variability at the molecular level in populations. Nevertheless, it is often impractical to examine long genomic stretches and a large number of individuals at the same time. In order to optimize this kind of study, we suggest a heuristic procedure for detection of the shortest region whose informational content can be considered sufficient for significant phylogenetic reconstruction. The method is based on the comparison of the pairwise genetic distances obtained from a set of sequences of reference to those obtained for different windows of variable size and position by means of a simple index. We also present an approach for testing whether the informative content in the stretches selected in this way is significantly different from the corresponding content shown by the larger genomic regions used as reference. Application of this test to the analysis of the VP1 protein gene of foot-and-mouth-disease type C virus allowed us to define optimal stretches whose informative content is not significantly different from that displayed by the complete VP1 sequence. We showed that the predictions made for type C sequences are valid for type O sequences, indicating that the results of the procedure are consistent.

Primary genetic characterization of HIV-1 isolates from WHO-sponsored vaccine evaluation sites by the RNase-A mismatch method

We have analyzed by the RNase-A mismatch method 35 isolates from four WHO-sponsored vaccine evaluation sites as a secondary laboratory of the WHO Network for HIV Isolation and Characterization. The application of an estimator for the establishment of genetic distances based on the RNase-A digestion patterns in combination with the phylogenetic analysis has allowed us to construct a tree with five well defined groups of viruses. Because the clustering with known reference strains, samples from Brazil could be grouped as subtype B and the majority of those from Thailand were subtype E. Some of the samples from Uganda were classified as subtype D. Isolates from Rwanda and some from Uganda were identified as subtype A viruses. These results coincide with data obtained by heteroduplex mobility assay and nucleotide sequencing in env regions. The RNase-A mismatch method combined with phylogenetic analysis permitted the primary genetic classification of 33 of 35 samples from the WHO Network.

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.

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.

HIV type 1 variation in World Health Organization-sponsored vaccine evaluation sites: genetic screening, sequence analysis, and preliminary biological characterization of selected viral strains. WHO Network for HIV Isolation and Characterization

A laboratory network has been established by the World Health Organization (WHO) to systematically isolate and characterize HIV strains from different parts of the world, and to obtain information and reagents that would facilitate HIV vaccine development. Sixty-three HIV-1 isolates obtained from 224 specimens collected during 1992-1993 in Brazil, Rwanda, Thailand, and Uganda were characterized in this initial study. Virus strains were first genetically subtyped using three different screening methodologies: PCR-gag fingerprinting, RNase A mismatch, and heteroduplex mobility assay (HMA). In addition, selected viruses were sequenced in V3 (52 strains), C2-V3 (42 strains), gp120 (15 strains), and/or gp160 (8 strains) regions of their envelope genes. These studies identified viruses belonging to different sequence subtypes in the four countries: 16 subtype B and 1 subtype C strains in Brazil, 13 subtype A strains in Rwanda, 15 subtype E and 2 subtype B strains in Thailand, and 3 subtype A and 13 subtype D strains in Uganda. Comparison of sequence data with results from the genetic screening efforts identified the HMA as a rapid and reliable method for sequence subtype determinations. The majority of strains were collected from persons documented to have recently seroconverted to HIV-1 positivity, and most strains were found to have slow replication and low cytopathic characteristics and to be non-syncytium-inducing (slow/low-NSI phenotypes) in vitro, which, in many cases, correlated with the corresponding genotype and charge of the V3 loop amino acid sequences. This collection of HIV strains is presently being characterized immunologically and serologically, including neutralization assays, to define whether there are immunological correlates of the sequence subtypes. Identification of potential immunotypes would be of considerable importance for the further development of HIV vaccines.