Epidemiology and genotypic diversity of human metapneumovirus in paediatric patients with acute respiratory infection in Beijing, China

Abstract

Background: Acute respiratory tract infections (ARTIs) causes high amounts of morbidity and mortality worldwide every year. Human metapneumovirus (HMPV) is a major pathogen of ARTIs in children. In this study, we aimed to investigate the epidemiology and genotypic diversity of HMPV in children hospitalized with ARTIs in Beijing, China.

Methods: Hospitalized children aged < 14 years with ARTIs were enrolled from April 2017 to March 2018; nasopharyngeal aspirates were collected and subjected to real-time polymerase chain reaction tests for HMPV. HMPV-positive samples were genotyped based on a partial N gene. Whole genome sequences were determined for samples with high viral loads.

Results: 4.08% (52/1276) enrolled paediatric patients were identified as having HMPV infection. The epidemic season is winter and early spring, children aged ≤ 4 years were more susceptible to HMPV infection (47/52, 90.38%). The co-infection rate were 36.54% (19/52), the most common co-infected virus were influenza and respiratory syncytial virus. The main diagnoses of HMPV infection were pneumonia (29/52, 55.77%) and bronchitis (23/52, 44.23%), while the main clinical manifestations were cough, fever, rhinorrhoea, and sneeze. Among 48 HMPV-positive specimens, A2b (19/48, 39.58%) and B1 (26/48, 54.17%) were the main epidemic subtypes. Patients with HMPV genotype A infection had a higher viral load compared to genotype B patients (6.07 vs. 5.37 log₁₀ RNA copies/ml). Five complete sequences of HMPV were obtained. This is the first report of a whole genome sequence of HMPV-B1 isolated in China.

Conclusions: HMPV is an important respiratory pathogen in paediatric patients. Cases of HMPV infection could burden hospitals in the epidemic season. HMPV viral loads and genotypes have no correlation with co-infection or clinical characteristics.

Keywords: Epidemiology; Genetic diversity; Human metapneumovirus; Pediatric; Respiratory tract infection.

Fig. 1

Seasonal distribution of HMPV-positive specimens from April 2017 and March 2018

Fig. 2

HMPV viral loads in NPAs from patients with or without co-infections. Numbers 1–5 represent samples from which the whole genome sequence is obtained

Fig. 3

Phylogenetic relationships of the strains detected in HMPV-infected children. a NJ-tree constructed based on the partial N gene sequences (813 bp) of HMPV strains. b NJ-tree constructed based on the whole genome sequences of HMPV strains. The reference strain is marked with a ▲, and the strains analysed in this study are marked with ●. The country of origin for each reference and sample sequence is indicated by the following country codes: AR, Argentina; AU, Australia; CA, Canada; CN, China; JP, Japan; NL, Netherlands; PE, Peru; and US, United States of America