Genomic Surveillance of Yellow Fever Virus Epizootic in São Paulo, Brazil, 2016 - 2018.

São Paulo, a densely inhabited state in southeast Brazil that contains the fourth most populated city in the world, recently experienced its largest yellow fever virus (YFV) outbreak in decades. YFV does not normally circulate extensively in São Paulo, so most people were unvaccinated when the outbreak began. Surveillance in non-human primates (NHPs) is important for determining the magnitude and geographic extent of an epizootic, thereby helping to evaluate the risk of YFV spillover to humans. Data from infected NHPs can give more accurate insights into YFV spread than when using data from human cases alone. To contextualise human cases, identify epizootic foci and uncover the rate and direction of YFV spread in São Paulo, we generated and analysed virus genomic data and epizootic case data from NHPs in São Paulo. We report the occurrence of three spatiotemporally distinct phases of the outbreak in São Paulo prior to February 2018. We generated 51 new virus genomes from YFV positive cases identified in 23 different municipalities in São Paulo, mostly sampled from NHPs between October 2016 and January 2018. Although we observe substantial heterogeneity in lineage dispersal velocities between phylogenetic branches, continuous phylogeographic analyses of generated YFV genomes suggest that YFV lineages spread in São Paulo at a mean rate of approximately 1km per day during all phases of the outbreak. Viral lineages from the first epizootic phase in northern São Paulo subsequently dispersed towards the south of the state to cause the second and third epizootic phases there. This alters our understanding of how YFV was introduced into the densely populated south of São Paulo state. Our results shed light on the sylvatic transmission of YFV in highly fragmented forested regions in São Paulo state and highlight the importance of continued surveillance of zoonotic pathogens in sentinel species.

Zoonotic Malaria Risk in Serra Do Mar, Atlantic Forest, Brazil.

Here, the main goal is to assess natural infections of Plasmodium spp. in anophelines in a forest reserve from the same region where we previously found a surprisingly high rate (5.2%) of plasmodia infections (n = 25) in Kerteszia mosquitoes (N = 480) on the slopes of Serra do Mar, Atlantic Forest, Brazil. The mosquito collection sampling was carried out at the Legado das Águas Forest Reserve using CDC light traps and Shannon traps at night (5-10 pm) in 3-day collections in November 2021 and March, April, May, and November 2022. The captured specimens were morphologically identified at the species level and had their genomic DNA extracted in pools of up to 10 mosquitoes/pool. Each pool was tested using 18S qPCR and cytb nested PCR plus sequencing. A total of 5301 mosquitoes, mostly belonging to the genus Kerteszia (99.7%), were sampled and sorted into 773 pools. Eight pools positive for Plasmodium spp. were identified: four for Plasmodium spp., one for P. vivax or P. simium, one for P. malariae or P. brasilianum, and two for the P. falciparum-like parasite. After Sanger sequencing, two results were further confirmed: P. vivax or P. simium and P. malariae or P. brasilianum. The minimum infection rate for Kerteszia mosquitoes was 0.15% (eight positive pools/5285 Kerteszia mosquitoes). The study reveals a lower-than-expected natural infection rate (expected = 5.2% vs. observed = 0.15%). This low rate relates to the absence of Alouatta monkeys as the main simian malaria reservoir in the studied region. Their absence was due to a significant population decline following the reemergence of yellow fever virus outbreaks in the Atlantic Forest from 2016 to 2019. However, this also indicates the existence of alternative reservoirs to infect Kerteszia mosquitoes. The found zoonotic species of Plasmodium, including the P. falciparum-like parasite, may represent a simian malaria risk and thus a challenge for malaria elimination in Brazil.

Mapping environmental suitability of Haemagogus and Sabethes spp. mosquitoes to understand sylvatic transmission risk of yellow fever virus in Brazil.

BACKGROUND: Yellow fever (YF) is an arboviral disease which is endemic to Brazil due to a sylvatic transmission cycle maintained by infected mosquito vectors, non-human primate (NHP) hosts, and humans. Despite the existence of an effective vaccine, recent sporadic YF epidemics have underscored concerns about sylvatic vector surveillance, as very little is known about their spatial distribution. Here, we model and map the environmental suitability of YF's main vectors in Brazil, Haemagogus spp. and Sabethes spp., and use human population and NHP data to identify locations prone to transmission and spillover risk. METHODOLOGY/PRINCIPAL FINDINGS: We compiled a comprehensive set of occurrence records on Hg. janthinomys, Hg. leucocelaenus, and Sabethes spp. from 1991-2019 using primary and secondary data sources. Linking these data with selected environmental and land-cover variables, we adopted a stacked regression ensemble modelling approach (elastic-net regularized GLM, extreme gradient boosted regression trees, and random forest) to predict the environmental suitability of these species across Brazil at a 1 km x 1 km resolution. We show that while suitability for each species varies spatially, high suitability for all species was predicted in the Southeastern region where recent outbreaks have occurred. By integrating data on NHP host reservoirs and human populations, our risk maps further highlight municipalities within the region that are prone to transmission and spillover. CONCLUSIONS/SIGNIFICANCE: Our maps of sylvatic vector suitability can help elucidate potential locations of sylvatic reservoirs and be used as a tool to help mitigate risk of future YF outbreaks and assist in vector surveillance. Furthermore, at-risk regions identified from our work could help disease control and elucidate gaps in vaccination coverage and NHP host surveillance.

Reemergence of Yellow Fever in Brazil: The Role of Distinct Landscape Fragmentation Thresholds.

Yellow Fever Virus (YFV) reemergence in Brazil was followed by human suffering and the loss of biodiversity of neotropical simians on the Atlantic coast. The underlying mechanisms were investigated with special focus on distinct landscape fragmentation thresholds in the affected municipalities. An ecological study in epidemiology is employed to assess the statistical relationship between events of YFV and forest fragmentation in municipal landscapes. Negative binomial regression model showed that highly fragmented forest cover was associated with an 85% increase of events of YFV in humans and simians (RR = 1.85, CI 95% = 1.24-2.75, p=0.003) adjusted by vaccine coverage, population size, and municipality area. Intermediate levels of forest cover combined with higher levels of forest edge densities contribute to the YFV dispersion and the exponential growth of YF cases. Strategies for forest conservation are necessary for the control and prevention of YF and other zoonotic diseases that can spillover from the fragmented forest remains to populated cities of the Brazilian Atlantic coast.

Entomological investigation of a sylvatic yellow fever area in São Paulo State, Brazil.

Following reports of two autochthonous cases of sylvatic yellow fever in the State of São Paulo, Brazil, in 2000, entomological surveys were conducted with the objective of verifying the occurrence of vector species in forest environments close to or associated with riparian areas located in the western and northwestern regions of the State. Culicidae were captured in 39 sites distributed in four regions. Haemagogus leucocelaenus and Aedes albopictus were the most abundant species and were captured in all the regions studied. H. leucocelaenus was the most abundant species in the municipalities of Santa Albertina and Ouroeste, where the two cases of sylvatic yellow fever had been reported. Mosquitoes from the janthinomys/capricornii group were only found at eight sites in the São José do Rio Preto region, while Sabethes chloropterus was found at one site in Ribeirão Preto. H. leucocelaenus showed its capacity to adapt to a secondary and degraded environment. Our results indicate a wide receptive area for yellow fever transmission in the State of São Paulo, with particular emphasis on the possibility of H. leucocelaenus being involved in the maintenance of this sylvatic focus of the disease.

Natural infection in anopheline species and its implications for autochthonous malaria in the Atlantic Forest in Brazil.

BACKGROUND: A descriptive study was carried out in an area of the Atlantic Forest with autochthonous malaria in the Parelheiros subdistrict on the periphery of the municipality of São Paulo to identify anopheline fauna and anophelines naturally infected with Plasmodium as well as to discuss their role in this peculiar epidemiological context. METHODS: Entomological captures were made from May 2009 to April 2011 using Shannon traps and automatic CDC traps in four areas chosen for their different patterns of human presence and incidences of malaria (anthropic zone 1, anthropic zone 2, transition zone and sylvatic zone). Natural Plasmodium infection was detected by nested PCR based on amplification of the 18S rRNA gene. RESULTS: In total, 6,073 anophelines were collected from May 2009 to April 2011, and six species were identified in the four zones. Anopheles cruzii was the predominant species in the three environments but was more abundant in the sylvatic zone. Anopheles (Kerteszia) cruzii specimens from the anthropic and sylvatic zones were positive for P. vivax and P. malariae. An. (Ker.) bellator, An. (Nys.) triannulatus, An. (Nys.) strodei, An. (Nys.) lutzi and An. (Ano) maculipes were found in small numbers. Of these, An. (Nys.) triannulatus and An. (Nys.) lutzi, which were collected in the anthropic zone, were naturally infected with P. vivax while An. (Nys.) triannulatus from the anthropic zones and An. (Nys.) strodei from the transition zone were positive for P. malariae. CONCLUSION: These results confirm that Anopheles (Kerteszia) cruzii plays an important role as a major Plasmodium vector. However, the finding of other naturally infected species may indicate that secondary vectors are also involved in the transmission of malaria in the study areas. These findings can be expected to help in the implementation of new measures to control autochthonous malaria in areas of the Atlantic Forest.

Epidemiological and ecological aspects related to malaria in the area of influence of the lake at Porto Primavera dam, in western São Paulo State, Brazil.

A study was carried out in the area of influence of the Porto Primavera Hydroelectric Power Station, in western São Paulo State, to investigate ecological and epidemiological aspects of malaria in the area and monitor the profile of the anopheline populations following the environmental changes brought about by the construction of the lake. Mosquitoes captured were analyzed by standardized indicator species analysis (ISA) before and during different flooding phases (253 m and 257 m elevations). The local human population was studied by means of parasitological (thin/thick blood smears), molecular (PCR) and serological tests. Serological tests consisted of Enzyme Linked Immunosorbent Assay (ELISA) with synthetic peptides of the circumsporozoite protein (CSP) from classic Plasmodium vivax, P. vivax variants (VK247 and "vivax-like"), P. malariae and P. falciparum and Indirect Immunofluorescence Assay (IFA) with asexual forms of P. vivax, P. malariae and P. falciparum. The results of the entomological survey indicated that, although the Anopheles darlingi population increased after the flooding, the population density remained very low. No malaria, parasite infection or DNA was detected in the inhabitants of the study area. However, there was a low frequency of antibodies against asexual forms and a significant prevalence of antibodies against P. vivax, P. vivax variants, P. falciparum and P. malariae; the presence of these antibodies may result from recent or less recent contact with human or simian Plasmodium (a parallel study in the same area revealed the existence of a sylvatic cycle). Nevertheless, these results suggest that, as in other places where malaria is present and potential vectors circulate, the local epidemiological conditions observed could potentially support the transmission of malaria in Porto Primavera Lake if infected individuals are introduced in sufficient numbers. Further studies are required to elucidate the phenomena described in this paper.

Epidemiological and ecological aspects related to malaria in the area of influence of the lake at Porto Primavera dam, in western São Paulo State, Brazil / Aspectos epidemiológicos e ecológicos relacionados à malária na área de influência do lago da Represa de Porto Primavera, região oeste do Estado de São Paulo, Brasil

A study was carried out in the area of influence of the Porto Primavera Hydroelectric Power Station, in western São Paulo State, to investigate ecological and epidemiological aspects of malaria in the area and monitor the profile of the anopheline populations following the environmental changes brought about by the construction of the lake. Mosquitoes captured were analyzed by standardized indicator species analysis (ISA) before and during different flooding phases (253 m and 257 m elevations). The local human population was studied by means of parasitological (thin/thick blood smears), molecular (PCR) and serological tests. Serological tests consisted of Enzyme Linked Immunosorbent Assay (ELISA) with synthetic peptides of the circumsporozoite protein (CSP) from classic Plasmodium vivax, P. vivax variants (VK247 and "vivax-like"), P. malariae and P. falciparum and Indirect Immunofluorescence Assay (IFA) with asexual forms of P. vivax, P. malariae and P. falciparum. The results of the entomological survey indicated that, although the Anopheles darlingi population increased after the flooding, the population density remained very low. No malaria, parasite infection or DNA was detected in the inhabitants of the study area. However, there was a low frequency of antibodies against asexual forms and a significant prevalence of antibodies against P. vivax, P. vivax variants, P. falciparum and P. malariae; the presence of these antibodies may result from recent or less recent contact with human or simian Plasmodium (a parallel study in the same area revealed the existence of a sylvatic cycle) ...

Foi realizada pesquisa na área de influência do lago da Usina Hidrelétrica de Porto Primavera, região oeste do Estado de São Paulo, para estudar aspectos ecológicos e epidemiológicos da malária na localidade e acompanhar o perfil das populações de anofelinos frente às mudanças decorrentes do impacto ambiental pela formação do lago. Mosquitos capturados foram analisados pelo Índice de Abundância de Espécies Padronizado (IAEP), antes e durante o enchimento do reservatório (cotas 253 e 257 m). A população humana local foi estudada por meio de teste parasitológico (gota espessa e esfregaço sangüíneo), testes moleculares (PCR) e testes sorológicos. A sorologia consistiu na reação de ELISA com peptídeos sintéticos correspondentes à porção repetitiva da proteína circumsporozoíta (CSP) de Plasmodium vivax clássico, e suas variantes VK247 e "vivax-like", P. malariae e P. falciparum; e reação de Imunofluorescência Indireta (RIFI) com formas assexuadas de P. vivax, P. malariae e P. falciparum. Os resultados do estudo entomológico indicaram que, embora a população de Anopheles darlingi tenha aumentando após o enchimento, permaneceu em baixa densidade. Não foi detectada malária nem a presença de parasitos ou de DNA parasitário nos habitantes estudados. No entanto, foi observada baixa freqüência de anticorpos contra formas assexuadas e significativa prevalência de anticorpos contra esporozoítos de P. vivax e suas variantes, P. falciparum e P. malariae, que poderiam decorrer de contatos prévios, recentes ou não, com plasmódios humanos ou símios (o ciclo silvestre foi evidenciado em estudo paralelo realizado na mesma área)...

Entomological investigation of a sylvatic yellow fever area in Säo Paulo State, Brazil

O registro de dois casos autóctones de febre amarela silvestre no Estado de Säo Paulo, Brasil, em 2000, desencadeou investigaçöes entomológicas com o objetivo de verificar a ocorrência das espécies vetoras em ambientes florestais próximos ou associados às zonas ribeirinhas, situados nas regiöes oeste e noroeste do Estado. As capturas foram realizadas em 39 localidades distribuídas por quatro regiöes do Estado. Haemagogus leucocelaenus e Aedes albopictus foram as espécies mais abundantes e capturadas em todas as regiöes. H. leucocelaenus foi a espécie mais abundante nos municípios de Santa Albertina e Ouroeste, onde os casos de febre amarela silvestre foram registrados. Mosquitos do grupo janthinomys/capricornii foram encontrados em oito localidades de Säo José do Rio Preto, enquanto Sabethes chloropterus uma única vez em localidade de Ribeiräo Preto. Ficou evidenciada a aptidäo de H. leucocelaenus para adaptar-se a ambiente secundário e degradado. Nossos resultados apontam para uma ampla área receptiva para a transmissäo de febre amarela, com destaque para a possibilidade de H. leucocelaenus estar envolvido na manutençäo deste foco silvestre da doença.(AU)

Entomological investigation of a sylvatic yellow fever area in São Paulo State, Brazil

O registro de dois casos autóctones de febre amarela silvestre no Estado de São Paulo, Brasil, em 2000, desencadeou investigações entomológicas com o objetivo de verificar a ocorrência das espécies vetoras em ambientes florestais próximos ou associados às zonas ribeirinhas, situados nas regiões oeste e noroeste do Estado. As capturas foram realizadas em 39 localidades distribuídas por quatro regiões do Estado. Haemagogus leucocelaenus e Aedes albopictus foram as espécies mais abundantes e capturadas em todas as regiões. H. leucocelaenus foi a espécie mais abundante nos municípios de Santa Albertina e Ouroeste, onde os casos de febre amarela silvestre foram registrados. Mosquitos do grupo janthinomys/capricornii foram encontrados em oito localidades de São José do Rio Preto, enquanto Sabethes chloropterus uma única vez em localidade de Ribeirão Preto. Ficou evidenciada a aptidão de H. leucocelaenus para adaptar-se a ambiente secundário e degradado. Nossos resultados apontam para uma ampla área receptiva para a transmissão de febre amarela, com destaque para a possibilidade de H. leucocelaenus estar envolvido na manutenção deste foco silvestre da doença.