Epidemiology, Genomic Diversity, and Evolutionary Dynamics of Human Metapneumovirus Over 7 Years of Integrated Community- and Hospital-Based Sentinel Surveillance in Senegal, 2018-2024

In late 2024, a major human metapneumovirus (HMPV) outbreak in China caused widespread pneumonia and thousands of hospitalizations, drawing global attention to this virus. In Senegal, a concomitant rise in HMPV detections was observed in both community and hospital settings. This study aimed to describe the epidemiology, genomic diversity, and the evolutionary dynamics of HMPV strains circulating in Senegal over 7 years of integrated community- and hospital-based surveillance (2018-2024).

Nasopharyngeal samples were tested using multiplex real-time reverse transcription polymerase chain reaction. A subset of HMPV isolates underwent sequencing, followed by phylogenetic and Bayesian evolutionary analyses.

HMPV was detected in 3.3% (n = 19,204) of tested specimens. The highest positivity rate was observed among infants aged ≤ 11 months (31.2%), with decreasing rates in older age groups. Following COVID-19 related disruptions, HMPV circulation re-established a seasonal pattern after 2022, peaking during the rainy season. Genomic analyses revealed sustained cocirculation of sublineages A2b1, A2b2, B1, and B2, with periodic lineage replacement every 1-3 years. Genetic variability was predominantly observed in the G glycoprotein, with evidence of positive selection at codons 102, 153, 167, 169, 179, 181, and 202. Estimated evolutionary rates were 9.30 × 10^-4 substitutions per site per year for HMPV-A and 9.86 × 10^-4 substitutions per site per year for HMPV-B. Phylogeographic analyses indicate that HMPV epidemics in Senegal are driven by repeated introductions and ongoing exchange with other regions.

Our findings indicate sustained circulation and dynamic turnover of pre-existing sublineages rather than the emergence of a novel variant within the population, especially in infants aged ≤ 11 months.