Epidemiological and genomic investigation of chikungunya virus in Rio de Janeiro state, Brazil, between 2015 and 2018

Since 2014, Brazil has experienced an unprecedented epidemic caused by chikungunya virus (CHIKV), with several waves of East-Central-South-African (ECSA) lineage transmission reported across the country. In 2018, Rio de Janeiro state, the third most populous state in Brazil, reported 41% of all chikungunya cases in the country. Here we use evolutionary and epidemiological analysis to estimate the timescale of CHIKV-ECSA-American lineage and its epidemiological patterns in Rio de Janeiro. We show that the CHIKV-ECSA outbreak in Rio de Janeiro derived from two distinct clades introduced from the Northeast region in mid-2015 (clade RJ1, n = 63/67 genomes from Rio de Janeiro) and mid-2017 (clade RJ2, n = 4/67). We detected evidence for positive selection in non-structural proteins linked with viral replication in the RJ1 clade (clade-defining: nsP4-A481D) and the RJ2 clade (nsP1-D531G). Finally, we estimate the CHIKV-ECSA's basic reproduction number (R0) to be between 1.2 to 1.6 and show that its instantaneous reproduction number (Rt) displays a strong seasonal pattern with peaks in transmission coinciding with periods of high Aedes aegypti transmission potential. Our results highlight the need for continued genomic and epidemiological surveillance of CHIKV in Brazil, particularly during periods of high ecological suitability, and show that selective pressures underline the emergence and evolution of the large urban CHIKV-ECSA outbreak in Rio de Janeiro

Phylogenetic relationships of the New World titi monkeys (Callicebus): First appraisal of taxonomy based on molecular evidence

Background: Titi monkeys, Callicebus, comprise the most species-rich primate genus-34 species are currently recognised, five of them described since 2005. The lack of molecular data for titi monkeys has meant that little is known of their phylogenetic relationships and divergence times. To clarify their evolutionary history, we assembled a large molecular dataset by sequencing 20 nuclear and two mitochondrial loci for 15 species, including representatives from all recognised species groups. Phylogenetic relationships were inferred using concatenated maximum likelihood and Bayesian analyses, allowing us to evaluate the current taxonomic hypothesis for the genus. Results: Our results show four distinct Callicebus clades, for the most part concordant with the currently recognised morphological species-groups-the torquatus group, the personatus group, the donacophilus group, and the moloch group. The cupreus and moloch groups are not monophyletic, and all species of the formerly recognized cupreus group are reassigned to the moloch group. Two of the major divergence events are dated to the Miocene. The torquatus group, the oldest radiation, diverged c. 11 Ma; and the Atlantic forest personatus group split from the ancestor of all donacophilus and moloch species at 9-8 Ma. There is little molecular evidence for the separation of Callicebus caligatus and C. dubius, and we suggest that C. dubius should be considered a junior synonym of a polymorphic C. caligatus. Conclusions: Considering molecular, morphological and biogeographic evidence, we propose a new genus level taxonomy for titi monkeys: Cheracebus n. gen. in the Orinoco, Negro and upper Amazon basins (torquatus group), Callicebus Thomas, 1903, in the Atlantic Forest (personatus group), and Plecturocebus n. gen. in the Amazon basin and Chaco region (donacophilus and moloch groups). © 2016 Byrne et al

Terrestrial behavior in titi monkeys (Callicebus, Cheracebus, and Plecturocebus) : potential correlates, patterns, and differences between genera

For arboreal primates, ground use may increase dispersal opportunities, tolerance to habitat change, access to ground-based resources, and resilience to human disturbances, and so has conservation implications. We collated published and unpublished data from 86 studies across 65 localities to assess titi monkey (Callicebinae) terrestriality. We examined whether the frequency of terrestrial activity correlated with study duration (a proxy for sampling effort), rainfall level (a proxy for food availability seasonality), and forest height (a proxy for vertical niche dimension). Terrestrial activity was recorded frequently for Callicebus and Plecturocebus spp., but rarely for Cheracebus spp. Terrestrial resting, anti-predator behavior, geophagy, and playing frequencies in Callicebus and Plecturocebus spp., but feeding and moving differed. Callicebus spp. often ate or searched for new leaves terrestrially. Plecturocebus spp. descended primarily to ingest terrestrial invertebrates and soil. Study duration correlated positively and rainfall level negatively with terrestrial activity. Though differences in sampling effort and methods limited comparisons and interpretation, overall, titi monkeys commonly engaged in a variety of terrestrial activities. Terrestrial behavior in Callicebus and Plecturocebus capacities may bolster resistance to habitat fragmentation. However, it is uncertain if the low frequency of terrestriality recorded for Cheracebus spp. is a genus-specific trait associated with a more basal phylogenetic position, or because studies of this genus occurred in pristine habitats. Observations of terrestrial behavior increased with increasing sampling effort and decreasing food availability. Overall, we found a high frequency of terrestrial behavior in titi monkeys, unlike that observed in other pitheciids

Population parameters of the endangered titi monkey, Callicebus coimbrai Kobayashi and Langguth, 1999, in the fragmented landscape of southern Sergipe, Brazil

The recently-discovered titi, Callicebus coimbrai, is endemic to the coastal Brazilian Atlantic Forest south of the São Francisco River, a region with a long tradition of deforestation. While a number of C. coimbrai populations have now been identified, little is known about basic population parameters. Considering the importance of this information for conservation planning, the population of a site in southern Sergipe (with a total area of forest of approximately 500 ha) was surveyed between April and October 2008. Standard line transect procedures were used in the four largest fragments, and additional monitoring included the use of playback broadcasts for the observation of titi groups. The presence of titis was confirmed in all the forest fragments at the site, including one of only five hectares. Two other primates - Callithrix jacchus and Cebus xanthosternos - were also recorded at the site, but were less abundant than titis. A total transect walk of 476 km provided 164 sightings of primates, the majority of which (104) were of Callicebus coimbrai. Titi groups ranged in size between two and five individuals. The most reliable estimate of overall population density, derived from the combined data set, was 12.6 individuals per km²;, although density was much higher in smaller (more disturbed) fragments. The total population of Callicebus coimbrai at the site was estimated to be at least 50 individuals, which may represent a considerable proportion of the population of the species remaining in the wild. In addition to its apparent tolerance of habitat fragmentation, densities of C. coimbrai recorded at the site compare favourably with those of other Atlantic Forest titi species

Population parameters of the endangered titi monkey, Callicebus coimbrai Kobayashi and Langguth, 1999, in the fragmented landscape of southern Sergipe, Brazil

The recently-discovered titi, Callicebus coimbrai, is endemic to the coastal Brazilian Atlantic Forest south of the São Francisco River, a region with a long tradition of deforestation. While a number of C. coimbrai populations have now been identified, little is known about basic population parameters. Considering the importance of this information for conservation planning, the population of a site in southern Sergipe (with a total area of forest of approximately 500 ha) was surveyed between April and October 2008. Standard line transect procedures were used in the four largest fragments, and additional monitoring included the use of playback broadcasts for the observation of titi groups. The presence of titis was confirmed in all the forest fragments at the site, including one of only five hectares. Two other primates - Callithrix jacchus and Cebus xanthosternos - were also recorded at the site, but were less abundant than titis. A total transect walk of 476 km provided 164 sightings of primates, the majority of which (104) were of Callicebus coimbrai. Titi groups ranged in size between two and five individuals. The most reliable estimate of overall population density, derived from the combined data set, was 12.6 individuals per km²;, although density was much higher in smaller (more disturbed) fragments. The total population of Callicebus coimbrai at the site was estimated to be at least 50 individuals, which may represent a considerable proportion of the population of the species remaining in the wild. In addition to its apparent tolerance of habitat fragmentation, densities of C. coimbrai recorded at the site compare favourably with those of other Atlantic Forest titi species