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Epidemiological, Clinical and Genotypic Features of Human Metapneumovirus in Patients with Influenza-Like Illness in Senegal, 20

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Epidemiological, Clinical and Genotypic Features of Human Metapneumovirus in Patients with Influenza-Like Illness in Senegal, 20 Jallow et al. BMC Infectious Diseases (2019) 19:457 https://doi.org/10.1186/s12879-019-4096-y RESEARCHARTICLE Open Access Epidemiological, clinical and genotypic features of human Metapneumovirus in patients with influenza-like illness in Senegal, 2012 to 2016 Mamadou Malado Jallow1, Amary Fall1, Davy Kiori1, Sara Sy1, Déborah Goudiaby1, Mamadou Aliou Barry2, Malick Fall3, Mbayame Ndiaye Niang1 and Ndongo Dia1* 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. Keywords: Human metapneumovirus, Influenza-like illness, Epidemiology * Correspondence: [email protected] 1Département de Virologie, Institut Pasteur de Dakar, 36, Avenue Pasteur, B.P. 220, Dakar, Sénégal Full list of author information is available at the end of the article © The Author(s). 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Jallow et al. BMC Infectious Diseases (2019) 19:457 Page 2 of 9 Background and virological surveillance extended to other respiratory Human metapneumovirus (HMPV) was first observed in viruses diagnosis [9]. isolates of nasopharyngeal aspirate samples collected Briefly, all outpatients presenting to healthcare sentinel from children with lower respiratory tract infection dur- sites were screened for Influenza-like Illness (ILI) sur- ing the 1990s in Netherlands [1]. It is an enveloped, veillance. ILI was defined according to the Centers for non-segmented, negative-sense, single-stranded RNA Disease Control and Prevention (CDC) case definition: virus, and the first member of the new Metapneumo- sudden onset of fever (≥38 °C) with cough or sore throat virus genus belonging to the Paramyxoviridae family fewer than 3 days in duration. Naso-oropharyngeal that infects humans [2]. HMPV is a causal agent of acute swabs were collected from eligible participants, placed in respiratory infection (ARI) in primarily children [3]. The universal viral transport medium (Becton Dickinson and virus causes substantial morbidity especially in the ex- company, Italy), stored at 4-8°C, and then transported to tremes of age and in the immunocompromised [4]. For the NIC within the following 72 h for the testing. In instance, in hospitalized patients younger than 5 years of addition, demographic and clinical data were collected age, 5-7% of acute respiratory infections worldwide can from each patient. Once in the laboratory, specimens be attributed to hMPV [5]. At the clinical level, hMPV is were processed immediately for virus detection, identifi- associated to several diseases including bronchitis, cation, and characterization. Aliquots of each sample croup, pneumonia, bronchiolitis, reactive airway disease, were also stored at − 80 °C for biobanking or additional chronic obstructive pulmonary disease and asthma exac- analysis. erbations, specifically in children less than 5 years of age [6]. Despite the growing burden of diseases imputed to Detection of respiratory viruses this pathogen, there is no specific prophylactic vaccin- Total nucleic acid (DNA/RNA) extraction was per- ation strategy in place although various vaccine candi- formed from 200 μl of each sample using the QIAamp dates are currently under investigation [7]. In addition, Viral RNA kit (QIAGEN, Valencia, CA, USA) according little is known about the epidemiology of this virus, es- to the manufacturer’s instructions. For viral respiratory pecially in low income countries due to the low availabil- pathogens detection, the Anyplex™ II RV16 Detection kit ity of molecular diagnostic tools. (Seegene, Seoul, Korea) was used. The multiplex kit sys- To address this, we carried out a retrospective pilot tem enabled simultaneous detection of several respira- study, based on the processing of nasopharyngeal swabs, tory viruses: influenza A virus, influenza B virus, human with a focus on the epidemiology and molecular charac- respiratory syncytial virus (A and B), human adenovirus, teristics of HMPV in Senegal after 5 consecutive years of human metapneumovirus, human coronaviruses (229E, surveillance. We also evaluated the genetic variability in NL63 and OC43), human parainfluenza viruses (1, 2, 3 the Fusion protein (F) gene of HMPV detected. Phylo- and 4), human rhinovirus (A, B and C), human enterovi- genetic analysis based on the F gene was performed to ruses and human bocavirus. establish the relationships between Senegalese strains and previously described genotypes. Human Metapneumovirus molecular characterization and phylogenetic analysis Methods For the sequencing, 100 samples (20 per year) were ba- Study population and patient data collection sically selected upon three criteria: positivity for HMPV This retrospective study was conducted from January in real-time Polymerase Chain Reaction (PCR), year and 2012 to December 2016. It should be noted that samples week distribution of HMPV positive samples, and were collected in a sentinel flu monitoring context. Ct-values values detection (lowest Ct-values are corre- Senegal, a country with around 16 Million people and lated with important viral load). situated in the western part of Africa between the Atlan- Viral RNA from HMPV-positive samples was extracted tic Ocean and the Sahel, had a National Influenza Cen- and reverse transcribed to cDNA using RevertAid First ter since 1974. The NIC is hosted at the Institut Pasteur Strand cDNA Synthesis Kit (Thermo Scientific, Lithuania). Dakar (IPD) and had been part of the World Health A fragment of the hMPV F gene was targeted and amplified Organization (WHO) Global Influenza Surveillance Net- by nested PCR. The first amplification targeting a 750 bp work since 1996 [8]. The purpose of this influenza sur- fragment long was carried out using primers previously de- veillance has traditionally been the early detection of scribed [10].ThePhusionHigh-FidelityPCRMasterMix influenza epidemics in the community, the identification (New England Biolabs, Ipswich MA, USA) was used for of predominant circulating influenza strain, and the issu- amplifications. For each sample, PCR was carried out in a ing of public health recommendations. In 2012, the net- total reaction volume of 50 μl consisting of 15 μlH2O work has been consequently enhanced with RNase free, 2.5 μl of each primer (diluted at 10 μM), 25 μl epidemiological data collection, additional sentinel sites, of 2X Phusion Master Mix and 5 μl of cDNA template Jallow et al. BMC Infectious Diseases (2019) 19:457 Page 3 of 9 under the following cycling conditions: initial denaturation 2013 (18.5%), 1931 in 2014 (23.5%), 1718 in 2015 step of 15 min at 95 °C, followed by 35 PCR cycles includ- (20.9%) and 1828 in 2016 (22.3%). The male to female ing 30 s at 95 °C, 60 s at 55 °C, 60 s at 72 °C, and a final
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