Whole genome sequencing and evolution analyses of Human metapneumovirus

Abstract

Human metapneumovirus (HMPV) is a major pathogen of acute respiratory tract infections (ARTIs) in children. Whole genome sequence analyses could help understand the evolution and transmission events of this virus. In this study, we sequenced HMPV whole genomes to improve the identification of molecular epidemiology in Beijing, China. Nasopharyngeal aspirates of hospitalized children aged < 14 years old with ARTIs were screened for HMPV infection using qPCR. Fourteen pairs of overlapping primers were used to amplify whole genome sequences of HMPV from positive samples with high viral loads. The epidemiology of HMPV was analysed and 27 HMPV whole genome sequences were obtained. Sequence identity and the positional entropy analyses showed that most regions of HMPV genome are conserved, whereas the G gene contained many variations. Phylogenetic analysis identified 25 HMPV sequences that belonged to a newly defined subtype A2b1; G gene sequences from 24 of these contained a 111-nucleotide duplication. HMPV is an important respiratory pathogen in paediatric patients. The new subtype A2b1 with a 111-nucleotide duplication has become predominate in Beijing, China.

Keywords: Genetic diversity; Human metapneumovirus; Whole genome sequence.

Fig. 1

Sequence positional entropy (SPE) analyses of amino acid residues of the HMPV protein coding region

Fig. 2

Phylogenetic relationships of 27 HMPV strains. A Neighbor-joining (NJ)-tree based on the whole genome sequences. B NJ-tree based on the F gene sequences. The strains obtained in this study are marked with ●

Fig. 3

Demographic history of HMPV G gene. A Population growth inferred via a Bayesian Skyline coalescent tree. The blue lines represent the 95% highest probability density of the effective population size while the yellow line indicates the median of the size and genetic diversity of the population. B Maximum clade credibility tree of the HMPV G gene constructed using BEAST (version 1.10.5) under the skygrid nonparametric coalescent model. The green box indicates A2b1 180-nt-dup strains, and the yellow box indicates A2b1 111-nt-dup strains