Shi T, McLean K, Campbell H, Nair H. Aetiological role of common respiratory viruses in acute lower respiratory infections in children under five years: a systematic review and meta-analysis. J Glob Health. 2015;5(1):010408.
Article
PubMed
PubMed Central
Google Scholar
O’Brien KL, Baggett HC, Brooks WA, Feikin DR, Hammitt LL, Higdon MM, et al. Causes of severe pneumonia requiring hospital admission in children without HIV infection from Africa and Asia: the PERCH multi-country case-control study. Lancet. 2019;394(10200):757–79.
Article
Google Scholar
Moe N, Krokstad S, Stenseng IH, Christensen A, Skanke LH, Risnes KR, et al. Comparing human metapneumovirus and respiratory syncytial virus: viral codetections, genotypes and risk factors for severe disease. PLoS ONE. 2017;12(1):1–19.
Article
CAS
Google Scholar
Schildgen V, van den Hoogen B, Fouchier R, Tripp RA, Alvarez R, Manoha C, et al. Human metapneumovirus: lessons learned over the first decade. Clin Microbiol Rev. 2011;24(4):734–54.
Article
PubMed
PubMed Central
Google Scholar
Williams J, Shafagati N. Human metapneumovirus—what we know now. F1000Research. 2018;7:1–11.
Article
Google Scholar
Shi T, Arnott A, Semogas I, Falsey AR, Openshaw P, Wedzicha JA, Campbell H, Nair H. The etiological role of common respiratory viruses in acute respiratory infections in older adults: a systematic review and meta-analysis. J Infect Dis. 2020;222(Supplement_7):S563–9.
Article
PubMed
Google Scholar
Shi T, McAllister DA, O’Brien KL, Simoes EAF, Madhi SA, Gessner BD, et al. Global, regional, and national disease burden estimates of acute lower respiratory infections due to respiratory syncytial virus in young children in 2015: a systematic review and modelling study. Lancet. 2017;390(10098):946–58.
Article
PubMed
PubMed Central
Google Scholar
Glezen WP, Taber LH, Frank AL, Kasel JA. Risk of primary infection and reinfection with respiratory syncytial virus. Am J Dis Child. 1986;140(6):543–6.
CAS
PubMed
Google Scholar
Pavlin JA, Hickey AC, Ulbrandt N, Chan YP, Endy TP, Boukhvalova MS, Chunsuttiwat S, Nisalak A, Libraty DH, Green S, Rothman AL. Human metapneumovirus reinfection among children in Thailand determined by ELISA using purified soluble fusion protein. J Infect Dis. 2008;198(6):836–42.
Article
CAS
PubMed
Google Scholar
Li Y, Reeves RM, Wang X, Bassat Q, Brooks WA, Cohen C, Moore DP, Nunes M, Rath B, Campbell H, Nair H. Global patterns in monthly activity of influenza virus, respiratory syncytial virus, parainfluenza virus, and metapneumovirus: a systematic analysis. Lancet Glob Health. 2019;7(8):e1031–45.
Article
PubMed
Google Scholar
Hall CB, Douglas RG, Schnabel KC, Geiman JM. Infectivity of respiratory syncytial virus by various routes of inoculation. Infect Immun. 1981;33(3):779–83.
Article
CAS
PubMed
PubMed Central
Google Scholar
von Linstow M, Eugen-Olsen J, Koch A, Winther TN, Westh H, Hogh B. Excretion patterns of human metapneumovirus and respiratory syncytial virus among young children. Eur J Med Res. 2006;11(8):329.
Google Scholar
Boivin G, De Serres G, Hamelin ME, Côté S, Argouin M, Tremblay G, et al. An outbreak of severe respiratory tract infection due to human metapneumovirus in a long-term care facility. Clin Infect Dis. 2007;44(9):1152–8.
Article
PubMed
Google Scholar
Rima B, Collins P, Easton A, Fouchier R, Kurath G, Lamb RA, et al. ICTV virus taxonomy profile: Pneumoviridae. J Gen Virol. 2017;98(12):2912–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sullender WM. Respiratory syncytial virus genetic and antigenic diversity. Clin Microbiol Rev. 2000;13(1):1–15.
Article
CAS
PubMed
PubMed Central
Google Scholar
Van den Hoogen BG, Herfst S, Sprong L, Cane PA, Forleo-Neto E, De Swart RL, Osterhaus AD, Fouchier RA. Antigenic and genetic variability of human metapneumoviruses. Emerg Infect Dis. 2004;10(4):658.
Article
PubMed
PubMed Central
Google Scholar
Huck B, Scharf G, Neumann-Haefelin D, Puppe W, Weigl J, Falcone V. Novel human metapneumovirus sublineage. Emerg Infect Dis. 2006;12(1):147–50.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nao N, Saikusa M, Sato K, Sekizuka T, Usuku S, Tanaka N, et al. Recent molecular evolution of human metapneumovirus (HMPV): Subdivision of HMPV a2b strains. Microorganisms. 2020;8(9):1–14.
Article
CAS
Google Scholar
Melero JA, Garc B, Mart I, Pringle CR, Cane PA. Antigenic structure, evolution and immunobiology of human respiratory syncytial virus attachment (G) protein. J Gen Virol. 1997;78(10):2411–8.
Article
CAS
PubMed
Google Scholar
Goya S, Galiano M, Nauwelaers I, Trento A, Openshaw PJ, Mistchenko AS, Zambon M, Viegas M. Toward unified molecular surveillance of RSV: a proposal for genotype definition. Influenza Other Respir Viruses. 2020;14(3):274–85.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vandini S, Biagi C, Lanari M. Respiratory syncytial virus: The influence of serotype and genotype variability on clinical course of infection. Int J Mol Sci. 2017;18(8):1717.
Article
PubMed Central
CAS
Google Scholar
Agoti CN, Otieno JR, Ngama M, Mwihuri AG, Medley GF, Cane PA, et al. Successive respiratory syncytial virus epidemics in local populations arise from multiple variant introductions, providing insights into virus persistence. J Virol. 2015;89(22):11630–42.
Article
CAS
PubMed
PubMed Central
Google Scholar
Oketch JW, Kamau E, Otieno GP, Otieno JR, Agoti CN, Nokes DJ. Human metapneumovirus prevalence and patterns of subgroup persistence identified through surveillance of pediatric pneumonia hospital admissions in coastal Kenya, 2007–2016. BMC Infect Dis. 2019;19(1):1–13.
Article
Google Scholar
Bose ME, He J, Shrivastava S, Nelson MI, Bera J, Halpin RA, et al. Sequencing and analysis of globally obtained human respiratory syncytial virus a and B genomes. PLoS ONE. 2015;10(3):1–22.
Google Scholar
Lemey P, Rambaut A, Drummond AJ, Suchard MA. Bayesian phylogeography finds its roots. PLoS Comput Biol. 2009;5(9):e1000520.
Article
PubMed
PubMed Central
CAS
Google Scholar
Dudas G, Carvalho LM, Bedford T, Tatem AJ, Baele G, Faria NR, Park DJ, Ladner JT, Arias A, Asogun D, Bielejec F. Virus genomes reveal factors that spread and sustained the Ebola epidemic. Nature. 2017;544(7650):309–15.
Article
CAS
PubMed
PubMed Central
Google Scholar
Saikusa M, Nao N, Kawakami C, Usuku S, Sasao T, Toyozawa T, Takeda M, Okubo I. A novel 111-nucleotide duplication in the G gene of human metapneumovirus. Microbiol Immunol. 2017;61(11):507–12.
Article
CAS
PubMed
Google Scholar
Eshaghi A, Duvvuri VR, Lai R, Nadarajah JT, Li A, Patel SN, Low DE, Gubbay JB. Genetic variability of human respiratory syncytial virus A strains circulating in Ontario: a novel genotype with a 72 nucleotide G gene duplication. PLoS ONE. 2012;7(3):e32807.
Article
CAS
PubMed
PubMed Central
Google Scholar
Trento A, Galiano M, Videla C, Carballal G, García-Barreno B, Melero JA, Palomo C. Major changes in the G protein of human respiratory syncytial virus isolates introduced by a duplication of 60 nucleotides. J Gen Virol. 2003;84(11):3115–20.
Article
CAS
PubMed
Google Scholar
Levine OS, O’Brien KL, Deloria-Knoll M, Murdoch DR, Feikin DR, DeLuca AN, Driscoll AJ, Baggett HC, Brooks WA, Howie SR, Kotloff KL. The Pneumonia Etiology Research for Child Health Project: a 21st century childhood pneumonia etiology study. Clin Infect Dis. 2012;54(suppl_2):S93-101.
Article
PubMed
PubMed Central
Google Scholar
Deloria-Knoll M, Feikin DR, Scott JA, O’Brien KL, DeLuca AN, Driscoll AJ, Levine OS, Pneumonia Methods Working Group. Identification and selection of cases and controls in the Pneumonia Etiology Research for Child Health project. Clin Infect Dis. 2012;54(suppl2):S117–23.
Article
PubMed
PubMed Central
Google Scholar
Agoti CN, Mwihuri AG, Sande CJ, Onyango CO, Medley GF, Cane PA, et al. Genetic relatedness of infecting and reinfecting respiratory syncytial virus strains identified in a birth cohort from rural Kenya. J Infect Dis. 2012;206(10):1532–41.
Article
CAS
PubMed
PubMed Central
Google Scholar
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772–80.
Article
CAS
PubMed
PubMed Central
Google Scholar
Larsson A. AliView: a fast and lightweight alignment viewer and editor for large datasets. Bioinformatics. 2014;30(22):3276–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016;33(7):187.
Article
CAS
Google Scholar
Kalyaanamoorthy S, Minh BQ, Wong TK, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 2017;14(6):587–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nguyen LT, Schmidt HA, Von Haeseler A, Minh BQ. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32(1):268–74.
Article
CAS
PubMed
Google Scholar
Xie W, Lewis PO, Fan Y, Kuo L, Chen MH. Improving marginal likelihood estimation for Bayesian phylogenetic model selection. Syst Biol. 2011;60(2):150–60.
Article
PubMed
Google Scholar
Rambaut A, Lam TT, Max Carvalho L, Pybus OG. Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen). Virus Evol. 2016;2(1):007.
Article
Google Scholar
Lartillot N, Philippe H. Computing Bayes factors using thermodynamic integration. Syst Biol. 2006;55(2):195–207.
Article
PubMed
Google Scholar
Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst Biol. 2018;67(5):901.
Article
CAS
PubMed
PubMed Central
Google Scholar
Drummond AJ, Suchard MA, Xie D, Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol. 2012;29(8):1969–73.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bielejec F, Baele G, Vrancken B, Suchard MA, Rambaut A, Lemey P. SpreaD3: interactive visualization of spatiotemporal history and trait evolutionary processes. Mol Biol Evol. 2016;33(8):2167–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Owuor DC, de Laurent ZR, Kikwai GK, Mayieka LM, Ochieng M, Müller NF, Otieno NA, Hunsperger EN, Garten R, Barnes JR, Chaves SS. Characterizing the countrywide epidemic spread of influenza A (H1N1) pdm09 virus in Kenya between 2009 and 2018. medRxiv. 2021.
Giandhari J, Pillay S, Wilkinson E, Tegally H, Sinayskiy I, Schuld M, Lourenço J, Chimukangara B, Lessells RJ, Moosa Y, Gazy I. Early transmission of SARS-CoV-2 in South Africa: an epidemiological and phylogenetic report. medRxiv. 2020.
Bajunirwe F, Izudi J, Asiimwe S. Long-distance truck drivers and the increasing risk of COVID-19 spread in Uganda. Int J Infect Dis. 2020;1(98):191–3.
Article
CAS
Google Scholar
VelezRueda AJ, Mistchenko AS, Viegas M. Phylogenetic and phylodynamic analyses of human metapneumovirus in Buenos Aires (Argentina) for a three-year period (2009–2011). PLoS ONE. 2013;8(4):e63070.
Article
CAS
Google Scholar
Rojo GL, Goya S, Orellana M, Sancilio A, Perez AR, Montali C, García C, Sosa L, Musto A, Alvarez D, Castello A. Unravelling respiratory syncytial virus outbreaks in Buenos Aires, Argentina: molecular basis of the spatio-temporal transmission. Virology. 2017;1(508):118–26.
Article
CAS
Google Scholar
Zar Htwe KT, Dapat C, Shobugawa Y, Odagiri T, Hibino A, Kondo H, et al. Phylogeographic analysis of human influenza A and B viruses in Myanmar, 2010–2015. PLoS ONE. 2019;14(1):2010–5.
Google Scholar
Lemey P, Rambaut A, Bedford T, Faria N, Bielejec F, Baele G, et al. Unifying Viral Genetics and Human Transportation Data to Predict the Global Transmission Dynamics of Human Influenza H3N2. PLoS Pathog. 2014;10(2):e1003932.
Article
PubMed
PubMed Central
CAS
Google Scholar
Su YCF, Bahl J, Joseph U, Butt KM, Peck HA, Koay ESC, et al. Phylodynamics of H1N1/2009 influenza reveals the transition from host adaptation to immune-driven selection. Nat Commun. 2015;6:7952.
Article
CAS
PubMed
PubMed Central
Google Scholar
Flahaux ML, De Haas H. African migration: trends, patterns, drivers. Comp Migr Stud. 2016;4(1):1.
Article
PubMed Central
Google Scholar
De Maio N, Wu CH, O’Reilly KM, Wilson D. New routes to phylogeography: a Bayesian structured coalescent approximation. PLoS Genet. 2015;11(8):1–22.
Google Scholar
Baele G, Suchard MA, Rambaut A, Lemey P. Emerging concepts of data integration in pathogen phylodynamics. Syst Biol. 2017;66(1):e47-65.
PubMed
Google Scholar