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We conducted a retrospective phylogenetic analysis of Mayaro virus (MAYV) detected in French Guiana during 1996–2024. Analysis revealed circulation of MAYV genotype D sublineage 2 and suggested introduction from Brazil and spread to Haiti and Venezuela.
Phylogenetic findings support endemic circulation and reinforce the need for MAYV surveillance in the region. Mayaro virus (MAYV), a mosquitoborne RNA virus of the genus Alphavirus (family Togaviridae), causes acute febrile illness, often accompanied by prolonged arthralgia ( 1 ).
Identified in 1954 in Trinidad and Tobago, MAYV has caused sporadic outbreaks throughout Central and South America ( 2 – 5 ). Clinical manifestations of MAYV infection include fever, headache, myalgia, nausea, and persistent joint pain, sometimes lasting more than a year ( 6 , 7 ).
Among arboviruses in the Amazon region, MAYV and emerging Oropouche virus are considered to have the highest epidemic potential ( 1 , 2 ).
The analysis aims to illuminate viral lineage structure, introductions from neighboring regions, and patterns of local persistence, with emphasis on potential shifts in transmission dynamics and ecological niche adaptation.
The authors also seek to inform regional surveillance needs by clarifying phylogenetic relationships and biogeographic spread.
A total of 25 complete genomes were obtained from sampled cases, of which 24 were newly generated in this study; these genomes, together with 76 existing coding sequences from GenBank, formed a dataset of 100 sequences for analysis.
Consensus genomes were produced via the ARTIC pipeline and polished with Medaka; missing regions were completed via Sanger sequencing.
Recombination was assessed with Recombination Detection Program 4, revealing no recombination events among the French Guiana strains.
Time-scaled phylogenies were inferred under a general time-reversible model with gamma distributed rate variation and an invariable site component, using a strict molecular clock and Bayesian skyline prior.
Convergence diagnostics indicated adequate sampling (effective sample size > 200).
The work also references Bayesian maximum clade credibility trees for both the full 100-sequence dataset and the genotype D sublineage 2 subset.
Regional and cross-border relationships were assessed against a backdrop of 45 genotype D sublineage 2 sequences to bolster interpretation of introductions and spread.
Across the French Guiana isolates, there was a high degree of nucleotide similarity, indicating sustained local circulation with limited divergence over the studied period.
Sublineage 1 comprises strains from Peru, Brazil, Bolivia, and Venezuela, whereas sublineage 2 contains sequences from French Guiana, Brazil, Haiti, and Venezuela.
The first clade includes older Brazilian strains (1978) and French Guiana strains collected between 1999 and 2013, with an estimated tMRCA (time to most recent common ancestor) around 1951 (95% HPD 1934–1968).
The second clade comprises Brazilian strains from 1981–2012 alongside most French Guiana strains from 1996–2024, and also includes Haitian (2014) and Venezuelan (2016) strains that fall within the same French Guiana subclade.
The tMRCA for sublineage 2, clade 2 is around 1942 (95% HPD 1928–1956).
The clustering of Haitian and Venezuelan sequences within the French Guiana subclade suggests possible secondary exportation events; however, the authors caution that sampling bias cannot be excluded given limited recent genomic data.
Phylogeography indicates an expansion pattern: early clade 1 strains were largely inland or eastern, while clade 2 strains expanded westward toward urban coastal centers, including Cayenne and adjacent municipalities.
This is interpreted as persistent local transmission within a relatively stable ecological niche, with episodic emergence.
Experimental work shows urban vectors Aedes aegypti and Ae.
albopictus can be competent MAYV vectors, raising concerns about possible urbanization of transmission; however, these species were not present in French Guiana during the study window.
French Guiana-specific serologic data support endemic sylvatic transmission, with signals in 2020 suggesting an epidemiologic shift toward urban or periurban disease in line with observations for other arboviruses, though this study did not identify specific mutations associated with such a shift.
The analysis notes enhanced diagnostic capacity during the COVID-19 pandemic and concurrent dengue outbreaks as a possible contributor to improved case detection, which could partly explain the observed uptick.
Sublineage 1 strains primarily exhibited an STA motif, while sublineage 2 displayed greater diversity, including SMA and STV motifs, and the shared STV deletion.
Importantly, the authors observe that the STV deletion occurs in strains from both urban and remote forest locales, arguing against a straightforward link between this mutation and ecological shift or vector change.
The authors note potential limitations in inferring exact ecological or vector shifts from genomic data alone, given sampling density and genomic coverage limitations.
The authors explicitly acknowledge the possibility of sampling bias affecting the interpretation of cross-border transmission signals.
The sublineage relationships reflect plausible migration and persistence scenarios but are not definitive proof of specific transmission events.
It also highlights the need for continued and expanded genomic surveillance to clarify whether urban transmission is taking root or remains episodic.
This has implications for regional public health planning, emphasizing the importance of sustained genomic surveillance and arboviral monitoring compatible with sylvatic–urban interface dynamics.
These patterns suggest that surveillance programs in bordering regions and across the Caribbean and northern South American corridor may benefit from coordinated genomic and epidemiologic surveillance to detect introductions and track dissemination pathways.
The study highlights the need for vigilance regarding potential ecological shifts and the importance of integrating entomologic surveillance with genomic analyses to detect early signals of niche adaptation.
They emphasize that additional sequences, especially from Haiti, Venezuela, and Brazil in the relevant time frame, would improve confidence in exported lineage inferences and help disentangle sampling bias from true epidemiologic dynamics.
It states that some observations could be subject to revision with additional data or changed in final form.