Short Communication Evidence of rotavirus intragenic recombination between two sublineages of the same genotype Gabriel I. Parra, 1,2 Karin Bok, 3 3 Magaly Martı ´nez 1 and Jorge A. Gomez 3 Correspondence Gabriel I. Parra gabriel_parra@hotmail.com 1 Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asuncio ´n, Rı ´o de la Plata y Lagerenza, Asuncio ´ n (2511), Paraguay 2 Seccio ´ n Virologı ´a, Facultad de Ciencias, Universidad de la Repu ´ blica, Montevideo, Uruguay 3 Laboratorio de Gastroenteritis Virales, Departamento de Virologı ´a, INEI-ANLIS ‘Dr Carlos G. Malbra ´ n’, Buenos Aires, Argentina Received 25 November 2003 Accepted 10 February 2004 Rotavirus G4 prevalence increased during the past decade, with one of the highest prevalences reported during rotavirus surveillance in Argentina. Intragenotype diversity analysis has led to its subdivision into lineages (I and II) and sublineages (Ia–Id). On analysis of Argentine and G4 VP7 sequences from other locations, one Argentine strain (ArgRes1723) appeared to be an intermediate between G4 sublineages Ib and Ic. Similarity and bootscanning analyses and Sawyer’s test were carried out to demonstrate the recombinant nature of this strain. It was concluded that intragenic recombination occurred between sequences of sublineages Ib and Ic, with a crossover point between nucleotide positions 336 and 387. This study constitutes the first report of a mechanism of evolution in rotaviruses that is currently considered unusual – a recombination event between two strains of the same rotavirus genotype. These results will help increase current knowledge about rotavirus evolution and divergence, improving our understanding of the adaptation mechanisms used by these viruses. Rotaviruses are the major cause of gastroenteritis in infants and young children worldwide (Estes, 2001). They are members of the Reoviridae, containing 11 segments of double-stranded RNA enclosed in a triple-layered capsid. The rotavirus outer layer is constituted by two proteins, VP7 (glycoprotein) and VP4 (haemagglutinin). Both molecules independently induce protective neutralizing antibodies, leading to the classification of rotavirus into G (VP7) and P (VP4) types (Estes, 2001), and are also the main targets for current vaccine-development strategies (Cunliffe et al., 2002). At least 14 G types have been described so far, G1–G4 being the most common types found in humans worldwide (Desselberger et al., 2001). However, from season to season the prevalent G types found in a geographical region are different, exemplified by the great increase in prevalence of G4 detected worldwide during the past decade (Gentsch et al., 1996). One of the highest prevalences of G4 was reported in Argentina during national rotavirus surveillance (Bok et al., 2001). Studies of intragenotype diversity led to subdivision of the genotype into several lineages and sublineages, distinctly identified by unique genomic as well as epidemiological features. The phylo- genetic tree obtained from the analysis of genotype 4 VP7 gene nucleotide sequences distributed worldwide showed two major lineages, designated I and II. Lineage I was further subdivided into four sublineages, Ia–Id. Sublineages Ib and Ic were most commonly present in Argentina, and were also found to be associated with different characteristic rotavirus enterotoxins (NSP4) (K. Bok and others, unpublished data). It was noticeable that one strain, ArgRes1723, appeared to be an intermediate between sublineages Ib and Ic. Despite clustering with a high bootstrap value with sublineage Ib, it also presented the asparagine insertion (amino acid 76) characteristic of sublineage Ic (Bok et al., 2002). This interesting observation could be explained by two mechan- isms: intragenic recombination between strains from sub- lineages Ib and Ic; or sequence convergence (homoplasy) due to point mutations. Although genetic reassortment and nucleotide substitution are considered the most impor- tant mechanisms of evolution for rotaviruses (Estes, 2001; Gouvea & Brantly, 1995), Suzuki et al. (1998) have reported an intragenic recombination event between rotavirus strains of different serotypes. Many studies show the detection of mixed infections with two different serotypes infecting one individual, therefore increasing the probability of reassortment and/or recombination (Bok et al., 2001; Gouvea & Brantly, 1995; Jain et al., 2001). However, the detection of mixed infections with strains belonging to the same serotype has never been reported, as genotyping 3Present address: Center for Pediatric Research, Children’s Hospital of The King’s Daughters, Eastern Virginia Medical School, 855 West Brambleton Avenue, Norfolk, VA 23510, USA. An alignment of the nucleotide sequences of the VP7 gene of the 43 G4 rotaviruses used in the recombination analysis is available in JGV Online. 0007-9851 G 2004 SGM Printed in Great Britain 1713 Journal of General Virology (2004), 85, 1713–1716 DOI 10.1099/vir.0.79851-0