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.

Spatiotemporal dynamics and recurrence of chikungunya virus in Brazil: an epidemiological study.

BACKGROUND: Chikungunya virus (CHIKV) is an Aedes mosquito-borne virus that has caused large epidemics linked to acute, chronic, and severe clinical outcomes. Currently, Brazil has the highest number of chikungunya cases in the Americas. We aimed to investigate the spatiotemporal dynamics and recurrence pattern of chikungunya in Brazil since its introduction in 2013. METHODS: In this epidemiological study, we used CHIKV genomic sequencing data, CHIKV vector information, and aggregate clinical data on chikungunya cases from Brazil. The genomic data comprised 241 Brazilian CHIKV genome sequences from GenBank (n=180) and the 2022 CHIKV outbreak in Ceará state (n=61). The vector data (Breteau index and House index) were obtained from the Brazilian Ministry of Health for all 184 municipalities in Ceará state and 116 municipalities in Tocantins state in 2022. Epidemiological data on laboratory-confirmed cases of chikungunya between 2013 and 2022 were obtained from the Brazilian Ministry of Health and Laboratory of Public Health of Ceará. We assessed the spatiotemporal dynamics of chikungunya in Brazil via time series, mapping, age-sex distribution, cumulative case-fatality, linear correlation, logistic regression, and phylogenetic analyses. FINDINGS: Between March 3, 2013, and June 4, 2022, 253 545 laboratory-confirmed chikungunya cases were reported in 3316 (59·5%) of 5570 municipalities, mainly distributed in seven epidemic waves from 2016 to 2022. To date, Ceará in the northeast has been the most affected state, with 77 418 cases during the two largest epidemic waves in 2016 and 2017 and the third wave in 2022. From 2016 to 2022 in Ceará, the odds of being CHIKV-positive were higher in females than in males (odds ratio 0·87, 95% CI 0·85-0·89, p<0·0001), and the cumulative case-fatality ratio was 1·3 deaths per 1000 cases. Chikungunya recurrences in the states of Ceará, Tocantins (recurrence in 2022), and Pernambuco (recurrence in 2021) were limited to municipalities with few or no previously reported cases in the previous epidemic waves. The recurrence of chikungunya in Ceará in 2022 was associated with a new East-Central-South-African lineage. Population density metrics of the main CHIKV vector in Brazil, Aedes aegypti, were not correlated spatially with locations of chikungunya recurrence in Ceará and Tocantins. INTERPRETATION: Spatial heterogeneity of CHIKV spread and population immunity might explain the recurrence pattern of chikungunya in Brazil. These results can be used to inform public health interventions to prevent future chikungunya epidemic waves in urban settings. FUNDING: Global Virus Network, Burroughs Wellcome Fund, Wellcome Trust, US National Institutes of Health, São Paulo Research Foundation, Brazil Ministry of Education, UK Medical Research Council, Brazilian National Council for Scientific and Technological Development, and UK Royal Society. TRANSLATION: For the Portuguese translation of the abstract see Supplementary Materials section.

The taxonomic status of Skrjabinalius guevarai Gallego & Selva, 1979 (Nematoda: Pseudaliidae) and the synonymy of Skrjabinalius Delyamure, 1942 and Halocercus Baylis & Daubney, 1925.

Within the cetacean lungworm family Pseudaliidae Raillet & Henry, 1909, the distinction between the two genera of the subfamily Halocercinae Delamure, 1952, i.e. Halocercus Baylis & Daubney, 1925 and Skrjabinalius Delyamure, 1942, is principally based on the structure and shape of the male copulatory bursa. In species of Halocercus, the bursa is unlobed, whereas in the two species included in Skrjabinalius, S. cryptocephalus Delyamure, 1942 and Skrjabinalius guevarai Gallego & Selva, 1979, the bursa is described as clearly lobed. During a parasitological analysis of cetaceans from the Spanish Mediterranean, we collected a number of specimens of S. guevarai with variable levels of bursal lobulation, including individuals with unlobed bursae. Examination of voucher specimens of the type-species of Halocercus, H. delphini Baylis & Daubney, 1925, collected from cetaceans in the North-East Atlantic revealed the same variations in bursal shape, and the same arrangement of bursal rays and papillae. A morphometric comparison did not reveal substantial differences between both species. Moreover, Maximum Likelihood and Bayesian Inference analyses of the second internal transcribed spacer (ITS2) sequences of 11 specimens of S. guevarai and one of H. delphini grouped both species together, regardless of bursal shape, in a highly supported clade within the Pseudaliidae. Accordingly, we consider S. guevarai as a junior synonym of H. delphini. The great variability found in bursal lobulation in the type-species of Halocercus invalidates the use of this trait as a genus-level diagnostic character and, therefore, Skrjabinalius should also be considered synonymous with Halocercus.

Transmission and Predictors of Burden of Lungworms of the Striped Dolphin (Stenella coeruleoalba) in the Western Mediterranean.

Pseudaliid lungworms infect the lungs and sinuses of cetaceans. Information on the life cycle and epidemiology of pseudaliids is very scarce and mostly concerns species that infect coastal or inshore cetaceans. Available evidence indicates that some pseudaliids are vertically transmitted to the host, whereas others are acquired via infected prey. We documented pseudaliid infections in an oceanic cetacean, the striped dolphin (Stenella coeruleoalba) in the western Mediterranean, and investigated the possibilities of vertical vs. horizontal transmission and the potential influence of host body size, sex, and season on infection levels. We found two species of lungworm in 87 dolphins that stranded along the Spanish Mediterranean coast between 1987 and 2018. One or two larvae of Stenurus ovatus were found in three adult dolphins. Larger numbers of larvae and adults of Skrjabinalius guevarai were collected in 51 dolphins, including unweaned calves. These observations suggested that Skrjabinalius guevarai could be vertically transmitted. The abundance of Skrjabinalius guevarai increased significantly with host size, which suggested that it could be trophically transmitted, as well, with larger hosts consuming more infected prey. Infection levels peaked in spring, outside of the calving season, which is likely a reflection of a seasonal shift in dolphin diet. In summary, results indicate that Skrjabinalius guevarai was capable of both vertical and horizontal transmission, but future research should be directed at clarifying the potential mechanics behind transmission and intermediate hosts.