Epidemiological, clinical and genotypic features of human Metapneumovirus in patients with influenza-like illness in Senegal, 2012 to 2016

Abstract

Background Human metapneumovirus (HMPV) is a causal agent of acute respiratory infection, especially in primarily children. At the clinical level, HMPV is associated to several diseases including bronchitis, croup, pneumonia, bronchiolitis, reactive airway disease, chronic obstructive pulmonary disease and asthma exacerbations, specifically in children less than 5 years. Here, we carried out a retrospective pilot study, based on the processing of nasopharyngeal swabs, with a focus on the epidemiology and molecular characteristics of HMPV in Senegal. Methods This retrospective study was conducted from January 2012 to December 2016. Briefly, all outpatients presenting to healthcare sentinel sites were screened for surveillance enrollment and included if they met criteria for ILI. Naso-oropharyngeal swabs were collected from eligible participants. For viral respiratory pathogens detection, including HMPV, the Anyplex™ II RV16 Detection kit was used. A fragment of the hMPV F gene was targeted for sequencing. Results In total, 8209 patients with ILI were enrolled. Half of them (49.7%) were children under 5 years. Fever was the most common symptom followed by cough, and rhinitis. Three hundred eight patients were positive for HMPV (3.75%). 89 (28.9%) were detected as single infection. In co-infection cases, the most common co-infecting viruses were influenza, adenovirus and rhinovirus. HMPV detection rates in the different age groups varied significantly with the children under 5 years group accounting for 71.7% of positive patients. The temporal distribution pattern for HMPV infection showed a clear seasonal pattern with a higher activity during the rainy period (July–September). Phylogenetic analyses revealed that HMPV specimens circulating in Senegal were distributed into the two main genetic lineages, A and B. We also noted a co-circulation of both genetic lineages during the whole study period except in 2014. Conclusion In summary, the present study characterized the recent prevalence, seasonality and genetic diversity of HMPV in a large outpatient population presented with ILI in Senegal between 2012 and 2016. Globally our results show a clear seasonal circulation pattern of HMPV in Senegal. Our findings identified children less than 5 years as more susceptible group to HMPV infection. Molecular studies identified A2, B1 and B2 as the major genotypes circulating.

Recent Molecular Evolution of Human Metapneumovirus (HMPV): Subdivision of HMPV A2b Strains

“…In addition to the HMPV subtypes A2b1 and A2b2, another novel HMPV subtype A2c was recently reported [ 22 ]. To clarify the phylogenetic relationships among the HMPV strains, the genome sequences of the HMPV A2b2 and A2c strains from previous studies were obtained from the National Center for Biotechnology Information (NCBI) nucleotide sequence database ( ) [ 22 , 23 , 31 , 33 , 34 , 35 , 36 ]. Unfortunately, no full-genome sequences for HMPV A2b2 and A2c were available, so the phylogenetic analysis was performed using partial sequences of the F and G genes.…”

“…A consensus has been reached among researchers regarding these five HMPV subtypes. However, individual researchers have used different methods and gene regions or lengths when proposing new subtypes, such as A2c, A2b1, and A2b2 [ 22 , 23 , 31 , 33 , 34 , 35 , 36 ]. The “A2c” subtype was provisionally proposed based on analyses using only a short region (321 nucleotides in length) of the F gene and limited numbers of HMPV strains [ 22 ].…”

“…In 2012, the novel HMPV subtypes A2c, A2b1, and A2b2 were proposed based on phylogenetic analyses using a short region of the F gene and limited numbers of HMPV strains [ 22 , 23 ]. Recently, individual researchers have used different methods and gene regions or lengths when describing new subtypes, such as A2c, A2b1, and A2b2 [ 31 , 33 , 34 , 35 , 36 ]. However, a genome-wide phylogenetic and evolutionary analysis of recently proposed novel HMPV subtypes (A2c, A2b1, and A2b2) has not yet been performed, and detailed phylogenetic and evolutionary relationships between these subtypes are still unclear.…”

Detection of multiple viral sequences in the respiratory tract samples of suspected Middle East respiratory syndrome coronavirus patients in Jakarta, Indonesia 2015–2016

“…In the present study, HMPV was detected from a nasal swab of a 71-year-old patient with pneumonia. HMPV is one of the most significant causes of upper and lower respiratory tract infections in children and the elderly, especially the immunocompromised and those with underlying respiratory conditions (Oong et al, 2018;Taniguchi et al, 2019;Jallow et al, 2019). Two genotypes of HMPV have been identified, which can be classified into five lineages, A1, A2a, A2b, B1, and B2.…”

Identification of viral etiology of acute respiratory tract infections in children and adults in Tabanan, Bali, Indonesia

“…Using RSV PCR panel, we also detected seven HMPV all in children with three of them developing bronchopneumonia (data not shown). HMPV is known to pose significant threat causing upper and lower respiratory illness in children and elderly, especially those with underlying respiratory and immunocompromised conditions [26,27]. Two genotypes of HMPV have been identified to date, which can be classified into five lineages, A1, A2a, A2b, B1 and B2.…”