Spatial, temporal and evolutionary insight into seasonal epidemic Influenza A virus strains near the equatorial line: The case of Ecuador

Abstract

To study the spatial and temporal patterns of Influenza A virus (IAV) is essential for an efficient control of the disease caused by IAV and efficient vaccination programs. However, spatiotemporal patterns of spread as well as genetic lineage circulation of IAV on a countrywide scale have not been clearly determined for many tropical regions of the world. In order to gain insight into these matters, the spatial and temporal patterns of IAV in six different geographic regions of Ecuador, from 2011 to 2021, were determined and the timing and magnitude of IAV outbreaks in these localities investigated. The results of these studies revealed that although Ecuador is a South American country situated in the Equator line, its IAV epidemiology resembles that of temperate Northern Hemisphere countries. Phylogenetic analysis of H1N1pdm09 and H3N2 IAV strains isolated in five different localities of Ecuador revealed that provinces in the south of this country have the largest effective population size by comparison with provinces in the north, suggesting that the southern provinces may be acting as a source of IAV. Co-circulation of different H1N1pdm09 and H3N2 genetic lineages was observed in different geographic regions of Ecuador.

Keywords: Bayesian; Ecuador; Evolution; Influenza A virus; Time series.

Fig. 1

Seasonality of Influenza A in Ecuador (2011–2021). The periodic annual function obtained by summing the 12-monthly,6-monthly and 3-monthly harmonics is shown in orange. The original time series is shown in blue.

Fig. 2

Timing of the monthly primary and secondary peaks of Influenza A in six different Ecuadorian provinces. The timing of the primary and secondary peak against the latitudinal position of each province is shown. Primary peaks are shown by blue circles, while secondary peaks are shown by orange squares.

Fig. 3

Climatic parameters of Ecuadorian provinces. Mean monthly temperatures, precipitation and humidity in different Ecuadorian provinces are shown in A, B and C, respectively. Colors assigned to each province is indicated at the right of each graph.

Fig. 4

Bayesian MCMC phylogenetic tree analysis of IAV strains circulating in Ecuador. Maximum clade credibility trees obtained using the HKY+γ nucleotide model, a relaxed molecular clock and a structured coalescent method using MASCOT are shown. The trees are rooted to the Most Recent Common Ancestor (MRCA). Time to the MRCA is shown in years at the bottom of the figure. Bar at the bottom of the trees denote time in years. Numbers next to the branches show the median height of the branch. Strains in the tree are indicated by type and name followed by date of isolation. Nodes are colored according to the year of isolation. The results found for H1N1 and H3N2 strains are shown in (A) and (B), respectively.