Downloaded from www.microbiologyresearch.org by IP: 54.70.40.11 On: Thu, 03 Jan 2019 11:52:18 Journal of General Virology (2002), 83, 3103–3110. Printed in Great Britain ................................................................................................................................................................................................................................................................................... Genetic recombination in wild-type poliovirus George Dahourou, 1 † Sophie Guillot, 1 Olivier Le Gall 2 and Radu Crainic 1 1 Epide  miologie Mole  culaire des Ente  rovirus, Institut Pasteur, Paris, France 2 IPV, IBVM, INRA Bordeaux-Aquitaine, BP 81, 33883 Villenave d’Ornon Cedex, France Poliovirus isolates were screened for recombinants by combined analysis of two distant polymorphic segments of the poliovirus genome (one in the capsid and the other in the polymerase-coding region). Using a restriction fragment length polymorphism (RFLP) assay, a high number of recombinant genomes was found among vaccine-derived strains excreted by poliovirus vaccine vaccinees or vaccine-associated paralytic poliomyelitis cases. Some of these subjects carried a wild-type poliovirus (non-vaccine-specific) nucleotide sequence in the 3 part of the genome. Using a similar approach, a collection of wild-type poliovirus strains isolated in South India between 1985 and 1993 was screened for recombinants. Genotypes were defined by the parallel application of RFLP assays and genomic sequencing of the capsid protein VP1 and the 3D polymerase polypeptide. Analyses revealed several instances where the position of an isolate on the phylogenic tree for the capsid protein-coding segment did not agree with its position on the tree for the polymerase-coding region. In this way, several wild-type/wild-type and wild- type/vaccine recombinants could be identified, indicating that recombination is encountered commonly in the natural evolution of poliovirus strains. Introduction The genetic variability of picornaviruses is due mostly to nucleotide substitutions resulting from the high frequency of errors that occur during viral RNA replication (Holland et al., 1982 ; King et al., 1982 ; Kirkegaard & Baltimore, 1986). Genetic changes in poliovirus can also occur by molecular recombination (Cooper, 1977 ; Lai et al., 1992). In several recent studies on poliovirus genotypes, a high number of recombinant genomes was found among vaccine-derived strains excreted by oral poliovirus vaccine (OPV) vaccinees or vaccine- associated paralytic poliomyelitis (VAPP) cases. Among VAPP cases, up to 50 % of type 2 and 67 % of type 3 Sabin strains of poliovirus have been characterized as recombinant (Furione et al., 1993). Among them, a relatively high proportion [8 % in Furione et al. (1993)] were vaccinewild-type (VW) recom- binants carrying a non-vaccine-specific nucleotide sequence in the 3 part of the genome (Guillot et al., 2000). Administration of trivalent OPV provides optimal con- ditions for multiple infections of human intestinal target cells, thus favouring the possibility of intermolecular recombination Author for correspondence : George Dahourou. Fax 226 97 66 94. e-mail giorgiopasteur.fr †Present address : 01 BP 2198 Bobo Dioulasso, Burkina Faso, West Africa. between heterotypic viral genomes. This is enhanced under endemic conditions where different genotypes (homotypic or heterotypic) of wild-type strains are in circulation. Under these conditions, and knowing the natural spreading capacity of enteroviruses (Melnick, 1990), different possibilities of re- combination can occur between wild-type strains or both wild- type and vaccine-related strains. To date, many efforts have systematically searched viral genomes for evidence of recombination among RNA viruses in animals (Lai et al., 1992 ; Burke et al., 1997) and plants (Lai et al., 1992 ; Chenault & Melcher, 1994 ; Revers et al., 1996). The enterovirus group is particularly well suited to such research for several reasons. First, as mentioned above, a high proportion of recombinant genomes was found among vaccine-derived strains (Minor et al., 1986 ; Lipskaya et al., 1991 ; Furione et al., 1993 ; Georgescu et al., 1994). Second, enteroviruses are currently endemic in most developing countries and co-circulate in humans. Finally, for vaccine safety, it has been proposed that OPV should be replaced with a recombinant virus (displaying an enterovirus genome) to lower the rate of poliomyelitis in vaccine recipients (Gromeier et al., 1996). We have attempted to detect recombinant isolates in several wild-type poliovirus populations. Using combined analysis of two distant polymorphic segments of the viral genome (one in the capsid protein and the other in the polymerase-coding region), we screened 0001-8308  2002 SGM DBAD