Repeated introductions and widespread transmission of human metapneumovirus in Côte d’Ivoire

In Cote d'Ivoire, the incidence rate of acute respiratory infections (ARIs) rose from 165 cases per 1000 children in 2014 to more than 200 cases per 1000 children in 2015. The genetic diversity, transmission dynamics, and epidemiology of human metapneumovirus (hMPV), a causative agent of ARIs, in Cote d'Ivoire are unknown. This information is key in comprehending the transmission patterns and the role of global strains in establishing local epidemics in the country. Demographic information and biological samples were collected from 3,899 children under five-years-old, from January 1, 2013 to December 31, 2015 through Côte d'Ivoire's Influenza surveillance network. Phylodynamic modeling was performed on sequences of the surface and attachment glycoprotein genes (F and G, respectively). A total of 6.23% (n = 243/3899) of the samples were positive for hMPV. We observed continuous transmission of hMPV in Côte d'Ivoire throughout the year with peaks in the two dry periods from February to March and July to September. Phylodynamic modeling revealed the circulation of the two large groups of genotypes A and B as well as lineages A, B, B1, and B2. Viral introductions into Côte d'Ivoire were estimated to have occurred 2011-2015 for the F gene genotypes and 2007-2014 for G gene genotypes. Through phylogeographic modeling, we estimated at least 14 viral introductions into Côte d'Ivoire during this period frequently from regions with available sequence data (e.g., Asia). Molecular surveillance and characterization of the evolutionary mechanisms and the spread of hMPV in Côte d'Ivoire allows for differentiating the burden caused by this virus and other co-circulating respiratory viruses like RSV and influenza. Our findings may inform potential vaccine designs for hMPV similar to the recent success for RSV. Therefore, larger-scale and continuous genomic and epidemiological surveillance of hMPV globally and in Côte d'Ivoire is essential for identifying viral introductions and implementing control strategies.