Epidemiologic surveillance is essential for defining the burden, geographic distribution, and transmission patterns of human T-lymphotropic viruses (HTLVs) 1 and 2 (HTLV-1/2), particularly in underserved settings such as the Brazilian Amazon. Although Brazil is estimated to harbor the largest absolute number of HTLV-1 infections worldwide, data from urban Amazonian populations remain scarce (1,2). In this context, molecular surveillance is also critical because HTLV genetic diversity is geographically structured, could have clinical relevance, and helps refine understanding of lineage distribution and viral dissemination (3). We therefore investigated HTLV-1/2 infection in the metropolitan region of Manaus in the Amazonas state of Brazil and performed phylogenetic and phylogeographic analyses.

During May 2021–November 2023, we conducted a cross-sectional study of 1,397 residents of metropolitan Manaus recruited by convenience sampling across different city zones at universities, community centers, polyclinics, and primary healthcare units. Eligible participants were Manaus residents >7 years of age who voluntarily agreed to participate and provided written informed consent; for minors, we obtained parental or guardian consent and assent when applicable. We screened plasma samples for HTLV-1/2 antibodies by ELISA and confirmed seroreactive samples by Western blot or line immunoassay; indeterminate samples underwent molecular testing. We collected sociodemographic and behavioral data through a standardized questionnaire.

We amplified the 5′ long terminal repeat (LTR) region of HTLV-1 (579 bp) and HTLV-2 (788 bp) by nested PCR and sequenced the amplicons by Sanger sequencing. We inferred phylogenetic relationships by maximum-likelihood analysis in MEGA12 (https://www.megasoftware.net) using the Kimura 2-parameter model with 1,000 bootstrap replicates and a geographically diverse panel of HTLV-1 and HTLV-2 reference sequences retrieved from GenBank from a previously assembled dataset. We deposited sequences generated in this study into GenBank (accession nos. PV647910 for sequence WDM1168_BrMao, PV647909 for sequence WQC1199_BrMao, PV647908 for sequence SSS850_BrMao, and PV742404 for sequence JDC1001_BrMao). To investigate the timing and geographic history of HTLV-1 lineages, we performed Bayesian time-scaled phylogenetic and discrete phylogeographic analyses in BEAST X version 10.5 (https://beast.community).

Figure 1

Figure 1. Phylogenetic tree of HTLV isolates in study of emergence of West African HTLV-1aC subgroup, Brazilian Amazon. A) HTLV-1 sequences obtained in this study (bold text) were analyzed with 38 reference...

Overall HTLV-1/2 seroprevalence was 0.3% (95% CI 0.11%–0.73%; 4/1,397 participants), comprising 3 HTLV-1 and 1 HTLV-2 infections. All seropositive participants were >40 years of age and shared a profile of socioeconomic vulnerability: 75% were female, earned no more than minimum wage, had only elementary education, lacked marital partnerships, and relied on government assistance (Appendix). Phylogenetic analysis classified sequence SSS850_BrMao as HTLV-1aC, the West African subgroup, providing evidence of this lineage in the Brazilian Amazon (Figure 1, panel A). The remaining isolates were HTLV-1aA (WDM1168_BrMao and WQC1199_BrMao) and HTLV-2c (JDC1001_BrMao), indicating co-circulation of distinct HTLV lineages in this population (Figure 1).

Figure 2

Figure 2. Time-scaled phylogeny and discrete phylogeographic diffusion of HTLV-1 lineages in study of emergence of West African HTLV-1aC subgroup, Brazilian Amazon. A) Time-calibrated maximum clade credibility tree inferred in BEAST version...

After we identified the HTLV-1aC lineage, we performed Bayesian time-scaled phylogenetic and discrete phylogeographic analyses to infer its introduction and evolutionary history (Figure 2). Our results demonstrate that strain SSS850_BrMao clusters robustly within the HTLV-1aC clade, supporting its introduction into Amazonas around 2015 without evidence of intermediate dispersal through Pará. In contrast, 2 HTLV-1aA sequences clustered with reference sequences from Japan, indicating a separate introduction into northern Brazil via Pará (≈1971) followed by spread to Amazonas (≈1996). Together, those findings reveal >2 subtype-stratified introductions and identify HTLV-1aC as an epidemiologically relevant lineage in the region. However, because the phylogeographic inferences were based on a ≈579-bp 5′ LTR region fragment, they should be interpreted cautiously.

We observed a HTLV-1/2 prevalence in metropolitan Manaus, lower than estimates from other regions of Brazil, including Salvador and Mato Grosso do Sul (4,5). However, comparisons should be made with caution because sampling strategies and population composition differ across studies. Beyond prevalence, the key finding was detection of HTLV-1aC. Although this subgroup has previously been reported in Brazil by restriction fragment length polymorphism analysis (6), our study provides phylogenetically supported evidence of HTLV-1aC’s occurrence in the country and places it in phylogeographic context. This result broadens the known distribution of HTLV-1aC and suggests that viral diversity in northern Brazil may be greater than previously recognized, despite evidence that HTLV-1aA predominates nationwide (7,8). Phylogeographic analyses supported >2 subgroup-specific introductions into the region, highlighting HTLV-1aC as an epidemiologically relevant lineage. We also identified HTLV-2c in an urban resident, reinforcing evidence that this subtype is not restricted to Indigenous populations and might circulate across multiple epidemiologic settings in northern Brazil (9,10).

The first limitation of our study is that we used convenience sampling at multiple sites, rather than a population-based design. Therefore, the sample might not fully represent the city’s general population. The small number of positive participants precluded robust inference on risk factors or transmission routes. Phylogeographic reconstruction was further constrained by use of a short 5′ LTR fragment from a slowly evolving virus and by uneven regional sequence availability, reducing temporal and geographic resolution.

Despite those limitations, detection of HTLV-1aC in Manaus has surveillance relevance because rare lineages might remain unnoticed in settings with limited molecular monitoring. Broader epidemiologic surveillance combined with longer genomic regions and regionally representative sampling will be essential to refine lineage dispersion patterns, strengthen transmission hypotheses, and support HTLV prevention, diagnosis, and care policies tailored to the Brazilian Amazon.

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Suggested citation for this article: de Melo Silva J, Mourão EMV, Santos EM, Mineiro LS, de Souza PHR, de Oliveira LC, et al. Emergence of West African human T-lymphotropic virus 1aC subgroup, Brazilian Amazon. Emerg Infect Dis. 2026 Jul [date cited]. https://doi.org/10.3201/eid3207.260372