Whole Genome Sequencing and Phylogenetic Analyses of Sub-genotype A1 of the Human Metapneumovirus Detected in an Infant with Pneumonia

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The human metapneumovirus (HMPV) is an important pathogen in respiratory-tract infections in children. We undertook genomic sequence analyses and described the genetic characteristics of an uncommon sub-genotype, the HMPV A1 strain, and provide useful data for further studies. The HMPV A1(BJ-1610)strain was identified from a nasopharyngeal aspirate collected from a 3-month-old female with bronchopneumonia. Gene fragments of BJ-1610 were amplified by reverse transcription-polymerase chain reaction(RT-PCR)and assembled by DNAStar software. Sequence alignment for BJ-1610 and other HMPV reference strains with four known genotypes available in the GenBank database was conducted by DNAStar. Phylogenetic trees were created using MEGA 6.06 software. The whole genome of BJ-1610 was 13406nt in length (GenBank accession number:KU821121).Compared with HMPV reference strains,BJ-1610 shared the highest similarities with HMPV/AUS/150229278/2003/A(KC562226)from Australia, which was classified into sub-genotype A1.The nucleotide identity of the full genome between BJ-1610 and KC562226was 98.4%.N,P,F,M2-2and L genes had great similarity with KC562226 compared with other reference strains, whereas SH and G genes shared higher similarities with other strains of sub-genotype A1.Phylogenetic analyses of the whole genome showed that BJ-1610 was clustered into sub-genotype A1 and was close to KC562226.The N,P,M,F,M2-1,M2-2and L genes of BJ-1610 showed the same genetic features as the whole genome, whereas the variable genes SH and G were closest to KC403980.The F protein of BJ-1610 showed high genetic conservation. The length of the SH protein of BJ-1610 changed from 552 bp to 567 bp due to mutations in the stop codon. The amino-acid mutations on protein G led to a decrease in the number of N-glycosylation sites. As an infrequently circulating genotype, sequence analyses of the whole genome of a HMPV A1strain(BJ-1610)will promote further studies on its epidemiology and pathogenicity, and aid the development of vaccines and antiviral drugs.