Journal of Medical Virology 81:340–344 (2009) Genetic Variability of Human Metapneumovirus Isolated From Chilean Children, 2003–2004 Carola Escobar, 1 Vivian Luchsinger, 1 * Danielle Bruna de Oliveira, 2 Edison Durigon, 2 Jona ´ s Chnaiderman, 1 and Luis F. Avendan ˜o 1 1 Programa de Virologı´a, Instituto de Ciencias Biome´dicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile 2 Departamento de Microbiologı´a, Instituto de Ciencias Me´dicas II, Facultad de Medicina, Universidad de Sao Paulo, Sao Paulo, Brazil Human metapneumovirus (hMPV) is a significant cause of acute lower respiratory tract infection in all age groups, particularly in children. Two genetic groups and four subgroups of hMPV have been described. They co-circulate during an epidemic in variable proportions. The aims were to characterize the genotypes of hMPV recovered from children hospitalized for acute lower respi- ratory tract infection and to establish the molec- ular epidemiology of strains circulating in Santiago of Chile during a 2-year period. The detection of the N gene by reverse-transcription polymerase chain reaction was carried out for screening 545 infants hospitalized for acute lower respiratory tract infection in Santiago during 2003–2004. The genetic typing of hMPV was performed by analyzing the fusion gene sequen- ces. hMPV was detected in 10.2% (56/545 cases). Phylogenetic analysis of F gene sequences from 39 Chilean hMPV strains identified the two groups and four subgroups previously described. Strains clustered into group A were split further into the sub lineages A1, A2, and A3. Most Chilean strains clustered into the proposed novel A3 sub lineage (59%). A3 viruses were present in both years, while A1 and A2 circulated just in 1 year. In conclusion, hMPV is a relevant cause of acute lower respiratory infection in Chilean children and the potential novel cluster of group A emphasize the need for further regional genetic variability studies. J. Med. Virol. 81:340–344, 2009. ß 2008 Wiley-Liss, Inc. KEY WORDS: human metapneumovirus; Chile; genotypes INTRODUCTION Human metapneumovirus (hMPV) is a member of the family Paramyxoviridae, genus Metapneumovirus [Mackay et al., 2003]. It is an important etiological agent of acute lower respiratory tract infection in all age groups. hMPV was first identified in the Netherlands [van den Hoogen et al., 2001] and thereafter the virus has been detected worldwide [Peret et al., 2002; Stockton et al., 2002; Bastien et al., 2003; Osterhaus et al., 2003] at different rates depending upon age, gender, season and the diagnostic method used. In South America, hMPV has been reported in children at Brazil [Cuevas et al., 2003], Argentina [Galiano et al., 2004], Chile [Luchsinger et al., 2005] and Peru [Gray et al., 2006]. Likewise, there is serologic evidence of hMPV spread in Uruguay [Mirazo et al., 2005]. Many viral genes have been used to perform phylogenetic analyses, notably the F gene has been used widely for these purposes [Huck et al., 2006; Banerje et al., 2007; da Silva et al., 2008; Boivin et al., 2004]. Two groups and four subgroups (A1, A2, B1, and B2) have been identified. [van den Hoogen et al., 2004; Ludewick et al., 2005]; furthermore, new genetic clusters have been proposed in subgroup A2, designated A2a and A2b [Huck et al., 2006]. The F glycoprotein is highly conserved among hMPV strains, showing 95% identity at the amino acid level between the A and B groups; it is a major neutralization antigen that confers cross reactive protection among different lineages [Skiadopulos et al., 2004]. The aims of this report were to determine the frequency of hMPV in a Chilean population from 2003 through 2004 and to identify the subgroups circulating currently by analysis of F gene sequences. Abbreviations: hMPV, human metapneumovirus; IFA, indirect immunofluorescence assay; RSV, respiratory syncytial virus; PCR, polymerase chain reaction; N gene, nucleocapsid gene; MgCl 2 , magnesium chloride; F-gene, fusion protein gene; AMPV, avian metapneumovirus C. *Correspondence to: Vivian Luchsinger, MD, PhD, Programa de Virologı ´a, Instituto de Ciencias Biome ´dicas, Facultad de Medicina, Universidad de Chile, Independencia 1027, Indepen- dencia, Santiago, Chile. E-mail: vluchsin@med.uchile.cl Accepted 2 October 2008 DOI 10.1002/jmv.21399 Published online in Wiley InterScience (www.interscience.wiley.com) ß 2008 WILEY-LISS, INC.