Emergence of recombinant Mayaro virus strains from the Amazon basin

Abstract

Mayaro virus (MAYV), causative agent of Mayaro Fever, is an arbovirus transmitted by Haemagogus mosquitoes. Despite recent attention due to the identification of several cases in South and Central America and the Caribbean, limited information on MAYV evolution and epidemiology exists and represents a barrier to prevention of further spread. We present a thorough spatiotemporal evolutionary study of MAYV full-genome sequences collected over the last sixty years within South America and Haiti, revealing recent recombination events and adaptation to a broad host and vector range, including Aedes mosquito species. We employed a Bayesian phylogeography approach to characterize the emergence of recombinants in Brazil and Haiti and report evidence in favor of the putative role of human mobility in facilitating recombination among MAYV strains from geographically distinct regions. Spatiotemporal characteristics of recombination events and the emergence of this previously neglected virus in Haiti, a known hub for pathogen spread to the Americas, warrants close monitoring of MAYV infection in the immediate future.

Figure 1

Schematic representation of the identified recombination events associated with MAYV variants 2BR14 and HAITI15. (A) Identified recombinant sequences and fragments using various detection models. Significant p-values are indicated (alpha = 0.05), whereas ‘NS’ denotes the absence of statistical support (not significant). First recombination event based on dataset excluding 3BR61 sequence. (B) The first recombination event between the minor parental 30BR04 (red) and the major parental 3BR61 (green) gave rise to the recombinant strain 2BR14; the second recombination even between minor parental, 30BR04, and the major parental, the recombinant 2BR14, resulted in the recombinant strain HAITI15. Dotted blue lines indicate genomic breakpoints. The source of isolation of the strains is indicated with the schematic human, mosquito and tick black icons. Schematic representations are based on the results of recombination analysis in RDP4.

Figure 2

Detection of recombination in the MAYV genome using split-decomposition based networks. Network graphs were generated in SplitsTree based on the (A) full genome sequence, (B) genome sequence with recombinant regions as a result of the first recombination event removed, (C) genome sequence with recombinant region of the second recombination event removed, and (D) genome sequence with recombinant regions as a result of the first and second recombination events removed. The p-values of the Phi test of recombination for each genomic fragment are reported in each panel.

Figure 3

Maximum likelihood (ML) phylogenies of MAYV isolate full-genome, non-recombinant genomic fragment, and recombinant fragment sequences. ML trees were obtained for (A) full-genome, (B) non-recombinant genomic fragments, (C) recombinant fragments resulting from the first recombination event, and (D) recombinant fragments resulting from the second recombination event. The recombinant MAYV isolates are indicated by red lettering and highlighted in yellow, whereas the major and minor parental sequences are indicated by black lettering and highlighted in red and orange, respectively. (*) indicates strong statistical support along the branches defined by local or/and standard non-parametric bootstrap (BS) values > 75 or Shimodaira–Hasegawa-like approximate likelihood ratio test (SHa-LRT) > 95; (**) indicates very strong statistical support defined by local or/and standard non-parametric BS > 75 and SHa-LRT > 99.

Figure 4

Codon adaptability index (CAI) analysis for MAYV full-genome and gene sequences based on the codon usage of the most frequent genes of various host and vector species. CAI values based on full-genome, and nsP1 and E1 genes, reflecting the adaptation of MAYV genotypes L/D (yellow shade), L (blu shade), and D (pink shade) to human and non-primate hosts, and arthropod vectors. Values are reported as mean ± standard deviation, with the exception genotype L/D, for which only two sequences are available.

Figure 5

Bayesian phylogeographic analysis of MAYV non-recombinant fragment sequences. Time-scaled phylogenetic maximum clade credibility tree inferred using the Bayesian Skygrid demographic, strict molecular clock, and asymmetric phylogeographic diffusion models, implemented in BEAST v1.8.3. Branches are colored according to geographical location, and black diamonds represent branches supported by posterior probability > 0.99.

Figure 6

Schematic representation of the relationship between MAYV spread and human population connectivity and migration patterns among central South American and Haiti following the 2010 Haiti earthquake. (A) Time-scaled phylogenetic DensiTree representation of the Markov chain Monte Carlo sampled trees from the Bayesian posterior distribution. Branches are colored according to geographical location (legend at right). Well-supported branches are indicated by regions of high density (more solid color), whereas low-density regions (webs) indicate little agreement amongst the trees. (B) MAYV migration patterns inferred from Bayesian phylogeographic analysis using a discrete trait asymmetric diffusion model represented using SPREAD. Letters in bold indicate the major genotype circulating in each shaded area. (C) MAYV migration patterns superimposed onto the accessibility map of the Amazonian basin, and (D) compared to human migration started in 2010 from Haiti to Brazil and Peru, indicated by dotted green lines with directionality. Brazilian contribution to MINUSTAH personnel in Haiti during 2010–2015 is represented by green bubbles, with the size of each individual bubble corresponding to the number of uniformed personnel present during each year. MAYV migration patterns represented in (B,C and D) represent significant non-zero migration rates (Bayes Factor [BF] > 10), and are colored according to BF (legend at right). Maps were obtained from Google Maps (https://mapstyle.withgoogle.com), SPREAD software (www.kuleuven.be/aidslab/phylogeography/SPREAD.html), and ArcGIS database (https://www.arcgis.com) based on a previously published and available dataset (https://tiles.arcgis.com/tiles/P8Cok4qAP1sTVE59/arcgis/rest/services/Accessibility_Travel_time_to_Major_Cities/MapServer).