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Species belonging to the Leishmania (Viannia) subgenus are important causative agents of cutaneous and mucocutaneous leishmaniasis in Central and South America. These parasites possess several distinctive biological features that are influenced by their genetics, population structure, and genome instability. To date, several studies have revealed varying degrees of genetic diversity within Leishmania species. Particularly, in species of the L. (Viannia) subgenus, a generalized high intraspecific genetic diversity has been reported, although, conflicting conclusions have been drawn using different molecular techniques. Despite being the most common Leishmania species circulating in Panama and Colombia, few studies have analyzed clinical samples of Leishmania panamensis using whole-genome sequencing, and their restricted number of samples has limited the information they can provide to understand the population structure of L. panamensis. Here, we used next generation sequencing (NGS) to explore the genetic diversity of L. panamensis within its endemic range, analyzing data from 43 isolates of Colombian and Panamanian origin. Our results show the occurrence of three well-defined geographically correlated groups, and suggests the possible occurrence of additional phylogeographic groups. Furthermore, these results support the existence of a mixed mode of reproduction in L. panamensis, with varying frequencies of events of genetic recombination occurring primarily within subpopulations of closely related strains. This study offers important insights into the population genetics and reproduction mode of L. panamensis, paving the way to better understand their population structure and the emergence and maintenance of key eco-epidemiological traits.

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We performed a cross-sectional epidemiological study with 456 household dogs from urban and rural areas in two different regions situated at different altitudes in the state of Rio de Janeiro. The PCR technique using 18S rRNA as target revealed prevalence of 7.9% of dogs positive for piroplasmids. These samples were sequenced, and all the sequences were 99.9% to 100% similar to Babesia vogeli sequences from other countries. The spatial distribution of positive cases was analysed using kernel interpolation in the QGIS software, and the spatial correlation indicators among positive dogs, altitude, and presence of ticks were obtained by calculating the local Moran index using the GeoDa software. The spatial correlation between positive cases and altitude was clear based on both visual and statistical observations. Logistic regression applying the Wald method with a cutoff point of 0.1 revealed that dogs from a region with altitude <600 m had a 2.29-fold chance of B. vogeli infection (OR = 2.29; p-value = 0.04; CI: 1.03-5.07), while the rainy season was 2.45 times more associated with B. vogeli infection (OR = 2.45; p-value = 0.01; CI: 1.20-5.01), and dogs infested with Rhipicephalus sanguineus sensu lato had a 2.47 times higher chance of being infected (OR = 2.47; p-value = 0.02; CI: 1.13-5.38). Entropy analysis of the alignment between B. vogeli 18S rRNA (> 1.600 bp) sequences revealed that the most variable region corresponds to the hypervariable V4 region. Genetic homogeneity was observed among the B. vogeli 18S rRNA sequences, with distance values ranging from 0 to 0.007 and a mean value of 0.001. The evolutionary distance (0.003) was greater between the sequences from the municipalities of Barra do Pirai (low altitude) and Teresopolis (high altitude). This study expands the molecular epidemiologic knowledge of B. vogeli and shows points of variability in the B. vogeli 18S rRNA. The results indicate the potential use of spatial analysis tools to improve screening for positive cases, enabling more in-depth studies to strengthen understanding of tick infection prevention in dogs.

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Animal Trypanosomiasis (AT) is one of the most important problems in the Colombian livestock industry reducing its production around 30%. Caribbean and Orinoquia regions play a significant role in the development of this industry, having about 6.9 million cattle and 113,000 buffaloes. Considering the paucity in studies to understand the epidemiological features and control of AT in Colombia, the present study reports the seasonal transmission patterns and phylogeographic traits of the causal agents of AT in cattle and buffaloes from these regions. Between 2014 and 2016, a three-point longitudinal survey was designed to evaluate the mentioned characteristics. Molecular analysis in cattle showed an AT prevalence of 39.2% (T. theileri 38.6%, T. evansi 6.7% and T. vivax 0.2%), with higher values during wet and late wet seasons, while in buffaloes the prevalence was 28.2% (T. theileri 28.2% and T. evansi 1.3%), with higher values during the dry season. Additionally, variables such as tabanid abundance, vector control, breeding system, age and anemia signs were significantly associated with AT prevalence (P<0.05). Only T. theileri infection was higher in cattle with anemia signs than those with normal packed cell volume. Finally, phylogeographic analysis revealed that Colombian T. theileri isolates were associated to specific host genotypes IA and IIB, described worldwide; T. vivax isolates were related to the genotype from West Africa; while T. evansi isolates are related to the South American genotypes and to new genotypes. This is the first longitudinal survey that evaluates through molecular methods, the infection of Trypanosoma spp. in two important livestock regions from Colombia, showing that the clinical effects and prevalence of these trypanosomes in cattle and buffaloes are modulated by seasonal variations, host factors, and parasite traits. The results suggest that these factors have to be taken into account to successfully control AT in these regions.

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The HIV-1 clade C is prevalent worldwide and spread from Africa to South East Asia and South America early in the course of the epidemic. As a consequence of migration waves about 13% of the Italian HIV-1 epidemic is sustained by this clade. Two hundred fifty-four C pol sequences from the Italian ARCA database collected during 1997-2011 were analyzed. Epidemiological networks and geographical fluxes were identified through phylogeny using Bayesian approaches. Patients' country of origin was Italy, Africa, South America, and South East Asia for 44.9%, 23.6%, 4.7%, and 1.6%, respectively. Heterosexuals and men having sex with men accounted for 83.2% and 16.8%, respectively. Modality of infection was distributed differently: heterosexuals were largely prevalent among Italians (84.1%) and Africans (95.3%), while men having sex with men predominated among South Americans (66.7%). Eight significant clusters encompassing 111 patients (43.7%) were identified. Comparison between clustering and non-clustering patients indicated significant differences in country of origin, modality of infection and gender. Men having sex with men were associated to a higher probability to be included in networks (70% for men having sex with men vs. 30.3% for heterosexuals). Phylogeography highlighted two significant groups. One contained Indian strains and the second encompassed South Americans and almost all Italian strains. Phylogeography indicated that the spread of C subtype among Italians is related to South American variant. Although Italian patients mainly reported themselves as heterosexuals, homo-bisexual contacts were likely their source of infection. Phylogenetic monitoring is warranted to guide public health interventions aimed at controlling HIV infection.

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