Abstract
BackgroundHuman metapneumovirus (HMPV) is an important respiratory pathogen that causes seasonal epidemics of acute respiratory illness and contributes significantly to childhood pneumonia. Current knowledge and understanding on its patterns of spread, prevalence and persistence in communities in low resource settings is limited.MethodsWe present findings of a molecular-epidemiological analysis of nasal samples from children < 5 years of age admitted with syndromic pneumonia between 2007 and 2016 to Kilifi County Hospital, coastal Kenya. HMPV infection was detected using real-time RT-PCR and positives sequenced in the fusion (F) and attachment (G) genes followed by phylogenetic analysis. The association between disease severity and HMPV subgroup was assessed using Fisher’s exact test.ResultsOver 10 years, 274/6756 (4.1%) samples screened were HMPV positive. Annual prevalence fluctuated between years ranging 1.2 to 8.7% and lowest in the recent years (2014–2016). HMPV detections were most frequent between October of one year to April of the following year. Genotyping was successful for 205/274 (74.8%) positives revealing clades A2b (41.0%) and A2c (10.7%), and subgroups B1 (23.4%) and B2 (24.9%). The dominance patterns were: clade A2b between 2007 and 11, subgroup B1 between 2012 and 14, and clade A2c in more recent epidemics. Subgroup B2 viruses were present in all the years. Temporal phylogenetic clustering within the subgroups for both local and global sequence data was seen. Subgroups occurring in each epidemic season were comprised of multiple variants. Pneumonia severity did not vary by subgroup (p = 0.264). In both the F and G gene, the sequenced regions were found to be predominantly under purifying selection.ConclusionSubgroup patterns from this rural African setting temporally map with global strain distribution, suggesting a well-mixed global virus transmission pool of HMPV. Persistence in the local community is characterized by repeated introductions of HMPV variants from the global pool. The factors underlying the declining prevalence of HMPV in this population should be investigated.
Highlights
Human metapneumovirus (HMPV) is an important respiratory pathogen that causes seasonal epidemics of acute respiratory illness and contributes significantly to childhood pneumonia
HMPV prevalence in paediatric hospital admissions Between January 2007 and December 2016, 9079 individuals below 60 months of age were admitted to the paediatric wards at Kilifi County Hospital (KCH) with severe or very severe pneumonia
In conclusion, this report shows HMPV activity characterised by marked annual variation in occurrence, and in subgroup prevalence patterns gradual replacement of subgroups over time, and multiple circulating variants each epidemic varying year to year
Summary
Human metapneumovirus (HMPV) is an important respiratory pathogen that causes seasonal epidemics of acute respiratory illness and contributes significantly to childhood pneumonia. Human metapneumovirus (HMPV) is single-stranded, negative-sense RNA virus with a genome of about 13 kb [1, 2]. HMPV infections occur across all ages with severe disease predominantly occurring in children below 2 years of age and the elderly [3,4,5]. Since first description in 2001 [5], HMPV has been detected in all continents and its disease prevalence varies widely [6]. Clinical presentation of HMPV infection ranges from mild upper respiratory tract illness to severe lower respiratory tract disease [8] and overlaps with that of other common respiratory viruses especially respiratory syncytial virus (RSV) [9, 10]
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