Research

Genetic diversity and evolution of human metapneumovirus fusion protein over twenty years

Chin-Fen Yang^4* , Chiaoyin K Wang^4* , Sharon J Tollefson¹ , Rohith Piyaratna¹ , Linda D Lintao⁴ , Marla Chu⁴ , Alexis Liem⁴ , Mary Mark⁴ , Richard R Spaete⁴ , James E Crowe Jr^1,2,3 and John V Williams^1,2,3

¹  Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN, USA

²  Monroe Carell Jr Children's Hospital at Vanderbilt, Nashville, TN, USA

³  Department of Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA

⁴  MedImmune Vaccines, Inc, Mountain View, CA, USA

author email corresponding author email* Contributed equally

Virology Journal 2009, 6:138doi:10.1186/1743-422X-6-138

Published:	9 September 2009

Abstract

Background

Human metapneumovirus (HMPV) is an important cause of acute respiratory illness in children. We examined the diversity and molecular evolution of HMPV using 85 full-length F (fusion) gene sequences collected over a 20-year period.

Results

The F gene sequences fell into two major groups, each with two subgroups, which exhibited a mean of 96% identity by predicted amino acid sequences. Amino acid identity within and between subgroups was higher than nucleotide identity, suggesting structural or functional constraints on F protein diversity. There was minimal progressive drift over time, and the genetic lineages were stable over the 20-year period. Several canonical amino acid differences discriminated between major subgroups, and polymorphic variations tended to cluster in discrete regions. The estimated rate of mutation was 7.12 × 10^-4 substitutions/site/year and the estimated time to most recent common HMPV ancestor was 97 years (95% likelihood range 66-194 years). Analysis suggested that HMPV diverged from avian metapneumovirus type C (AMPV-C) 269 years ago (95% likelihood range 106-382 years).

Conclusion

HMPV F protein remains conserved over decades. HMPV appears to have diverged from AMPV-C fairly recently.