Genetic diversity, seasonality and transmission network of human metapneumovirus: identification of a unique sub-lineage of the fusion and attachment genes.

Human metapneumovirus (HMPV) is a single-stranded RNA virus classified in the Metapneumovirus genus within the Pneumovirinae sub-family of Paramyxoviridae. Since the first description of HMPV among children in the Netherlands1, the virus has emerged as one of the main causative agents of acute respiratory tract infections (RTIs) across all ages worldwide, in addition to the human respiratory syncytial virus (HRSV)2,3,4,5,6,7,8. The clinical presentation of acute and severe RTIs due to HMPV are strikingly similar to that of HRSV which are mainly characterised by mild respiratory illnesses to severe cough, bronchiolitis, pneumonia and often accompanied by high fever, myalgia and vomiting1. In the United States for example, the annual disease burden due to HMPV in hospitalized children below 5 years of age has been estimated at 1 per 1000 children, similar to that of the influenza virus9. HMPV is classified into two main genetic lineages denoted as genotypes A and B based on the phylogenetic analysis of the fusion (F) and attachment (G) genes. Each genotype is further classified into at least two sub-lineages – A1, A2, B1 and B210. It was later reported that two additional genetic sub-lineages were described within the A2 sub-lineage, named A2a and A2b based on the phylogenetic analysis of the nucleocapsid (N) and F gene sequences in a population of paediatric patients11. Different genetic sub-lineages of HMPV also co-circulate in a temporal fashion and a shift in the predominant circulating strain is not uncommon12,13,14. Acute respiratory infections caused by viruses such as HRSV, influenza A virus and human parainfluenza virus, amongst others are seasonally-distributed15. In temperate countries, a higher prevalence of HMPV has been reported during the months of winter and spring, with a lower seasonality than HRSV2,13,14,15,16. Climate also plays an important role in determining the seasonality of HMPV in tropical countries. Previous studies have described a direct correlation between the number of rainy days and the increase in the number of HMPV infections6,8. In addition to the number of rainy days, the effects of other important factors in a tropical climate such as the relative humidity, temperature and amount of rainfall on the prevalence of HMPV need to be investigated in order to provide a better understanding of its seasonality. Molecular epidemiological surveillance can be used to infer the dynamics of disease transmission based on the genetic relatedness of viral sequences derived from the population, as shown for human immunodeficiency virus (HIV)17,18,19, influenza virus20,21, echovirus22 and ebola virus23, amongst others. Although HMPV is one of the main causative agents of RTIs worldwide, little is known about the temporal dynamics of HMPV transmission in the population. Transmission networks inferred from the analysis of viral sequences elucidate the degree of the spread of an infection in a subset of the population that allows the identification of the population at high risk of transmitting the virus amongst each other, thus enabling the implementation of effective and targeted public health preventive measures to reduce the prevalence of new infections in the population at large17,18,24. To date, studies on the epidemiological distribution and genetic diversity of HMPV have been reported mainly among the hospitalised and outpatient children worldwide4,7,12,25,26. Despite the significant burden of acute RTIs due to HMPV9, information regarding the seasonal distribution, circulating genotypes and the dynamics of disease transmission of HMPV in the general population of all ages in tropical countries are currently limited6,8,27. In this study, we aimed to investigate the genetic diversity, seasonality and transmission network of HMPV infections among outpatient adults and children in Kuala Lumpur, Malaysia during a two-year period.