Anti-chikungunya virus seroprevalence in Indigenous groups in the São Francisco Valley,Brazil

BackgroundChikungunya fever (CHIKF) is a serious public health problem with a high rate of infection and chronic disabling manifestations that has affected more than 2 million people worldwide since 2005. In spite of this, epidemiological data on vulnerable groups such as Indigenous people are scarce, making it difficult to implement public policies in order to prevent this disease and assist these populations.ObjectiveTo describe the serological and epidemiological profile of chikungunya virus (CHIKV) in two Indigenous populations in Northeast Brazil, as well as in an urbanized control community, and to explore associations between CHIKV and anthropometric variables in these populations.Methodology/Principal findingsThis is a cross-sectional ancillary study of the Project of Atherosclerosis among Indigenous Populations (PAI) that included people 30 to 70 years old, recruited from two Indigenous tribes (the less urbanized Fulni-ô and the more urbanized Truká people) and an urbanized non-Indigenous control group from the same area. Subjects underwent clinical evaluation and were tested for anti-CHIKV IgG by enzyme-linked immunosorbent assay. Serological profile was described according to ethnicity, sex, and age. The study population included 433 individuals distributed as follows: 109 (25·2%) Truká, 272 (62·8%) Fulni-ô, and 52 (12%) from the non-Indigenous urbanized control group. Overall prevalence of CHIKV IgG in the study sample was 49.9% (216; 95% CI: 45·1–54·7). When the sample was stratified, positive CHIKV IgG was distributed as follows: no individuals in the Truká group, 78·3% (213/272; 95% CI: 72·9–83·1) in the Fulni-ô group, and 5.8% (3/52; 95% CI: 1.21–16) in the control group.Conclusions/SignificancePositive tests for CHIKV showed a very high prevalence in a traditional Indigenous population, in contrast to the absence of anti-CHIKV serology in the Truká people, who are more urbanized with respect to physical landscape, socio-cultural, and historical aspects, as well as a low prevalence in the non-Indigenous control group, although all groups are located in the same area.     

Detection and distribution of rotavirus in raw sewage and creeks in São Paulo, Brazil.

Rotaviruses were concentrated from 8-liter samples of raw domestic sewage and sewage-polluted creek water by adsorption to and elution from positively charged microporous filters (Zeta Plus 60S), followed by ultracentrifugation of the filter eluates. Indirect immunofluorescence and direct immunoperoxidase methods allowed detection and enumeration of rotavirus in 6 (20.6%) of 29 sewage samples and in 19 (34.5%) of 55 creek water samples. Levels of rotaviruses ranged from < 3 to 63 focus-forming units (FFU)/liter, and the geometric means were 2.2 FFU/liter in sewage, 2.9 FFU/liter at creek Tremembé, and 2.6 FFU/liter at creek Pirajussara. Wastewater samples examined during autumn and winter months showed a higher rate positivity for rotavirus than those collected in spring and summer, corresponding to the seasonal variation of rotaviral diarrhea in the city of São Paulo.     

Seropositivity for Coxiella burnetii in suspected patients with dengue in São Paulo state,Brazil

Q fever and brucellosis are zoonoses that cause fever and other systemic clinical signs in humans; their occurrences are neglected and the differential diagnosis for some diseases is disregarded. This study aimed to investigate the seropositivity for Coxiella burnetii and Brucella spp. antibodies in patients suspected of dengue from 38 municipalities in the state of São Paulo, Brazil. The samples (n = 604) were obtained by convenience from the Adolfo Lutz Institute serum bank. Sera were subjected to an indirect immunofluorescence assay (IFA) using in-house and commercial diagnostic protocols to evaluate C. burnetii positivity. For Brucella spp., sera were subjected to rapid plate serum agglutination with buffered acidified antigen (AAT), slow tube serum agglutination (SAL), and 2-mercaptoethanol (2-ME) techniques. Associations and statistical inferences of the results were performed by logistic regression according to the clinical and demographic variables collected from the patients. Statistical analyses were performed using Statistical Analysis Software (SAS) and associations were considered when p value was <0.05. In all, 129 patients showed positive results for Q fever, indicating a seropositivity of 21.4% (95% CI 18.15–24.85). Patients with 14–20 days of symptoms had 2.12 (95% CI 1.34–3.35) times more chances of being seropositive for Q fever than patients with 7–13 days, and patients with 21–27 days of fever had 2.62 (95% CI 1.27–5.41) times more chances of being seropositive for Q fever than patients with 7–13 days. For the other variables analyzed, there were no significant associations between the groups. No positivity for brucellosis was observed. This is the most comprehensive study of people seropositive for Q fever in São Paulo state and provides additional data for the medical community in Brazil. It is suggested that Q fever may be an important differential diagnosis of febrile illnesses in the region, demanding the government’s attention and investment in health.     

Isolation of Rickettsia rhipicephali and Rickettsia bellii from Haemaphysalis juxtakochi Ticks in the State of São Paulo, Brazil

In the present study, attempts to isolate Rickettsia in cell culture were performed individually in seven specimens of Haemaphysalis juxtakochi ticks collected in the state of São Paulo (southeastern Brazil). Rickettsia was successfully isolated by the shell vial technique and established in Vero cell culture from six ticks (six isolates). DNA extracted from infected cells of these isolates was tested by PCR and DNA sequencing, using genus-specific Rickettsia primers targeting the genes gltA, htrA, ompA, and ompB. After the generated sequences were compared with available sequences in GenBank, five out of the six isolates were identified as Rickettsia bellii (isolates HJ#1, HJ#2, HJ#3, HJ#4, and HJ#7). The sixth isolate (HJ#5) was closest to Rickettsia sp. strain R300, previously detected in H. juxtakochi in northern Brazil, and to Rickettsia rhipicephali, isolated from ticks in the United States. Following recent gene sequence-based criteria proposed for the identification of Rickettsia isolates, both isolate HJ#5 and strain R300 were identified as South American strains of R. rhipicephali, which was confirmed in this continent for the first time. Isolation of R. bellii from H. juxtakochi ticks, added to eight other tick species that have been reported to be infected with this bacterium in Brazil, indicates that R. bellii is indeed the most frequent Rickettsia species infecting ticks in Brazil. Currently, the role of both R. rhipicephali and R. bellii as human pathogens is regarded as unknown.     

Identifying Priority Giant Anteater (Myrmecophaga tridactyla) Populations for Conservation in São Paulo State,Brazil

Habitat loss is the main threat to biodiversity conservation worldwide. Some species may be particularly susceptible to the effects of fragmentation and the isolation of populations. The impacts of human activity on wild animal populations may be understood through relationships between individual genetic data and spatial landscape variables, particularly when considering local population dynamics influenced by fragmented habitats. Thus, the objective of this study was to analyze the population structure and genetic diversity of the giant anteater (Myrmecophaga tridactyla) using an individual sampling scheme (ISS) on a regional geographic scale. Data were collected from 41 specimens from twenty different locations in São Paulo State, Brazil, and six polymorphic microsatellite loci were genotyped. Our results indicate that barriers to gene flow exist and have segregated individuals of the farther away areas into two spatially structured clusters. The populations were also found to have high genetic diversity. The experimental sampling approach used herein enabled an analysis of the population dynamics of the giant anteater on a regional scale, as well as the identification of priority populations for genetic resource conservation for this species. The results reflect the need for adequate management plans. The efficacy of the sampling scheme may vary based on the study model used, but we argue that the use of an ISS combined with suitable molecular markers and statistical methods may serve as an important tool for initial analyses of threatened or vulnerable species, particularly in anthropized regions where populations are small or hard to characterize.     

High SARS-CoV-2 seroprevalence in persons experiencing homelessness and shelter workers from a day-shelter in São Paulo,Brazil

Brazil presents one of the highest COVID-19 death tolls in the world. The initial SARS-CoV-2 epicenter was São Paulo city. As of 2019, the homeless population of São Paulo city was estimated at 24,344 individuals, the largest national homeless population. The present study aimed to concomitantly assess the molecular and serological prevalence and associated risk factors of SARS-CoV-2 infection in a homeless population and related shelter workers from a day-shelter. Serum samples, nasopharyngeal and oropharyngeal swabs of persons who are homeless and shelter workers collected from August 25^th to 27^th, 2020 were tested for the presence of anti-SARS-CoV-2 IgM and IgG antibodies by ELISA and SARS-CoV-2 RNA by RT-qPCR, respectively. All swab samples tested negative by RT-qPCR. Seropositivity of IgM and IgG was 5/203 (2.5%) and 111/203 (54.7%) in persons who are homeless, and 5/87 (5.7%) and 41/87 (47.1%) in shelter workers, respectively, with no statistical differences between groups. The high seroprevalence found herein indicates early environmental and urban spreading of SARS-CoV-2, associated with sociodemographic and economic vulnerability.     

Assessing the areas under risk of invasion within islands through potential distribution modelling: The case of Pittosporum undulatum in São Miguel, Azores

Non-indigenous plant species have been frequently reported as successful invaders in island environments, changing plant community composition and structure. This is the case of the sweet pittosporum (Pittosporum undulatum), native from Australia, which is one of the most successful plant invaders in the Azores archipelago. Data extracted from recent forestry inventories were used to model and map the potential distribution of P. undulatum in São Miguel, the larger island of the Azores. Current distribution of P. undulatum is related to climate, altitude and some human activity effects. Further analysis of the areas under risk of invasion showed that protected areas are under potential threat, although only a few native forest remnants seem to be threatened due to future expansion of P. undulatum, since the current distribution of these native communities has been reduced due to clearing and competition with invasive plants. We discuss the threats that any further expansion of the species will represent for low-altitude native forests, as well as the utility of species distribution models in the assessment of the areas under risk of invasion.     

First occurrence of Cylindrospermopsin in the Azores (Lake São Brás,S. Miguel Island)

Limnology - Anthropogenic impacts have been reported as one of the main causes of eutrophication in freshwater systems and nutrient availability, mainly from discharges, are key to cyanobacteria...     

Active search strategies,clinicoimmunobiological determinants and training for implementation research confirm hidden endemic leprosy in inner São Paulo,Brazil

BackgroundThis study evaluates implementation strategies for leprosy diagnosis based on responses to a Leprosy Suspicion Questionnaire (LSQ), and analyzes immunoepidemiological aspects and follow-up of individuals living in a presumptively nonendemic area in Brazil.Methodology/Principal findingsQuasi-experimental study based on LSQ throughout Jardinópolis town by community health agents, theoretical-practical trainings for primary care teams, dermatoneurological examination, anti-PGL-I serology, RLEP-PCR, and spatial epidemiology. A Leprosy Group (LG, n = 64) and Non-Leprosy Group (NLG, n = 415) were established. Overall, 3,241 LSQs were distributed; 1,054 (32.5%) LSQ were positive for signs/symptoms (LSQ+). Among LSQ+ respondents, Q2-Tingling (pricking)? (11.8%); Q4-Spots on the skin? (11.7%); Q7-Pain in the nerves? (11.6%); Q1-Numbness in your hands and/or feet? (10.7%) and Q8-Swelling of hands and feet? (8.5%) were most frequently reported symptoms. We evaluated 479 (14.8%) individuals and diagnosed 64 new cases, a general new case detection rate (NCDR) of 13.4%; 60 were among 300 LSQ+ (NCDR-20%), while 4 were among 179 LSQ negative (NCDR-2.23%). In LG, Q7(65%), Q2(60%), Q1(45%), Q4(40%) and Q8(25%) were most frequent. All 2x2 crossings of these 5 questions showed a relative risk for leprosy ranging from 3 to 5.8 compared with NLG. All patients were multibacillary and presented hypochromatic macules with loss of sensation. LG anti-PGL-I titers were higher than NLG, while 8.9% were positive for RLEP-PCR. The leprosy cases and anti-PGL-I spatial mappings demonstrated the disease spread across the town.Conclusions/SignificanceImplementation actions, primarily LSQ administration focused on neurological symptoms, indicate hidden endemic leprosy in a nonendemic Brazilian state.     

Biofilms as major sources of Legionella spp. in hydrothermal areas and their dispersion into stream water

Abstract Water and biofilms from two hydrothermal areas in central Portugal, and one hydrothermal area in New Mexico, USA, were examined for Legionella spp. In general, Legionella spp were isolated in higher numbers from biofilms than from water, although one biofilm with a temperature of 50°C, did not yield isolates of these organisms. In one area L. pneumophila serogroup (sg) 3 constituted the major population in the thermal discharge by the stream and the biofilm below it; however, L. pneumophila sg 1 was predominant in the sediments of the stream bed with minor thermal springs below the main discharge and in the water downstream. No Legionellae were isolated from water upstream of the hydrothermal area indicating that the thermal area was the source of the organisms in the stream water. In the other two hydrothermal areas, L. pneumophila sg 1 constituted the major population isolated, whereas L. pneumophila sg 3 was absent or isolated in low numbers. Isolates of L. micdadei were also recovered from one hydrothermal area, while ‘ L. londoniensis ’ was isolated from another.     

Cases and distribution of visceral leishmaniasis in western São Paulo: A neglected disease in this region of Brazil

Visceral leishmaniasis (VL) is one of the most prevalent parasitic diseases worldwide. In 2019, 97% of the total numbers of cases in Latin America were reported in Brazil. In São Paulo state, currently 17.6% of infected individuals live in the western region. To study this neglected disease on a regional scale, we describe the spread of VL in 45 municipalities of the Regional Network for Health Assistance11(RNHA11). Environmental, human VL (HVL), and canine VL (CVL) cases, Human Development Index, and Lutzomyia longipalpis databases were obtained from public agencies. Global Moran’s I index and local indicators of spatial association (LISA) statistics were used to identify spatial autocorrelation and to generate maps for the identification of VL clusters. On a local scale, we determined the spread of VL in the city of Teodoro Sampaio, part of the Pontal of Paranapanema. In Teodoro Sampaio, monthly peri-domicile sand fly collection; ELISA, IFAT and Rapid Test serological CVL; and ELISA HVL serum surveys were carried out. In RNHA11 from 2000 to 2018, Lu. longipalpis was found in 77.8%, CVL in 69%, and HVL in 42.2% of the 45 municipalities, and 537 individuals were notified with HVL. Dispersion occurred from the epicenter in the north to Teodoro Sampaio, in the south, where Lu. longipalpis and CVL were found in 2010, HVL in 2018, and critical hotspots of CVL were found in the periphery. Moran’s Global Index showed a weak but statistically significant spatial autocorrelation related to cases of CVL (I = 0.2572), and 11 municipalities were identified as priority areas for implementing surveillance and control actions. In RNHA11, a complex array of socioeconomic and environmental factors may be fueling the epidemic and sustaining endemic transmission of VL, adding to the study of a neglected disease in a region of São Paulo, Brazil.     

Avian disease surveillance on the island of San Cristóbal,Galápagos

Endemic island species face unprecedented threats, with many populations in decline or at risk of extinction. One important threat is the introduction of novel and potentially devastating diseases, made more pressing due to accelerating global connectivity, urban development, and climatic changes. In the Galápagos archipelago two important wildlife diseases: avian pox (Avipoxvirus spp.) and avian malaria (Plasmodium spp. and related Haemosporidia) challenge endemic species. San Cristóbal island has seen a paucity of disease surveillance in avian populations, despite the island''s connectedness to the continent and the wider archipelago. To survey prevalence and better understand the dynamics of these two diseases on San Cristóbal, we captured 1205 birds of 11 species on the island between 2016 and 2020. Study sites included urban and rural lowland localities as well as rural highland sites in 2019. Of 995 blood samples screened for avian haemosporidia, none tested positive for infection. In contrast, evidence of past and active pox infection was observed in 97 birds and identified as strains Gal1 and Gal2. Active pox prevalence differed significantly with contemporary climatic conditions, being highest during El Niño events (~11% in 2016 and in 2019 versus <1% in the La Niña year of 2018). Pox prevalence was also higher at urban sites than rural (11% to 4%, in 2019) and prevalence varied between host species, ranging from 12% in medium ground finches (Geospiza fortis) to 4% in Yellow Warblers (Setophaga petechial aureola). In the most common infected species (Small Ground Finch: Geospiza fuliginosa), birds recovered from pox had significantly longer wings, which may suggest a selective cost to infection. These results illustrate the threat future climate changes and urbanization may present in influencing disease dynamics in the Galápagos, while also highlighting unknowns regarding species‐specific susceptibilities to avian pox and the transmission dynamics facilitating outbreaks within these iconic species.     

Shell occupancy of the intertidal hermit crab Clibanarius erythropus (Decapoda,Diogenidae) on São Miguel (Azores)

The intertidal hermit crab Clibanarius erythropus was collected at three sites on São Miguel (Azores) during low spring tides. Shells occupied were identified and measured. Crab sizes ranged from 1.78 to 13.67 mm (cephalothoracic shield length), with an average size of 4.40 ± 1.44 mm. Of the 19 different shells utilised, the most frequent were Littorina striata (23.8%), Nassarius incrassatus (22.5%) and Mitra sp. (22.0%). At Fenais da Luz, L. striata was most frequently occupied, while at Água de Alto it was N. incrassatus and, at Caloura, Mitra sp. shells were most frequently used. Shell selection appears to be determined by respective sizes of hermit crab and shell species. Small size-class crabs occupy more shell species than larger crabs. The smallest crab was found at Fenais da Luz occupying a small Bittium sp., whereas the largest crab was found at Caloura inhabiting Stramonita haemastoma.     

Genomic features and copper biosorption potential of a new Alcanivorax sp. VBW004 isolated from the shallow hydrothermal vent (Azores,Portugal)

A new Alcanivorax sp. VBW004 was isolated from a shallow hydrothermal vent in Azores Island, Portugal. In this study, we determined VBW004 was resistant to copper. This strain showed maximum tolerance of copper concentrations up to 600 μg/mL. Based on 16S rRNA gene sequencing and phylogeny revealed that this strain was more closely related to Alcanivorax borkumensis SK2. We sequenced the genome of this strain that consist of 3.8 Mb size with a G + C content of 58.4 %. In addition, digital DNA-DNA hybridizations (dDDH) and the average nucleotide identities (ANI) analysis between Alcanivorax borkumensis SK2 and Alcanivorax jadensis T9 revealed that Alcanivorax sp. VBW004 belongs to new species. Functional annotation revealed that the genome acquired multiple copper resistance encoding genes that could assist VBW004 to respond to high Cu toxicity. Our results from biosorption analysis presumed that the VBW004 is an ecologically important bacterium that could be useful for copper bioremediation.     

Genetic structure of Flores island (Azores, Portugal) in the 19th century and in the present day: evidence from surname analysis

The island of Flores is the most westerly of the Azores archipelago (Portugal). Despite its marked geographic isolation and reduced population size, biodemographic and genetic studies conducted so far do not support the idea that its population constitutes a genetic isolate. In this study we conducted a surname analysis of the Flores population for two time periods: the second half of the 19th century and the present day. Our main purposes were (1) to biodemographically and genetically characterize the island, taking into account the strong reduction in population observed from the middle of the 19th century to the present day; and (2) to analyze the influence that the effective population size and geographic distance have on the genetic structure of populations. For both periods analyzed, all indicators of diversity revealed a high level of surname diversity. Our results are in accordance with the diversity estimates obtained from both monoparental genetic markers located in the Y chromosome and frequencies of mtDNA haplogroups. Contrary to what could be expected, considering the strong reduction of population in the last 150 years, we observed that diversity was maintained and that microdifferentiation decreased. Both observations support a higher openness of parishes as a consequence of the increase in communication routes. From the first to the second period analyzed, a change in surname composition is evident, although the more frequent surnames in Flores are almost the same for both periods and some of them are reported to be surnames present in the first settlers of Flores. This result testifies to the impact of founders on the present-day gene pool of Flores island and allows us to infer that the genetic characterization of the present-day population of Flores could provide reliable information about the history of the peopling of the Azores.     

Mutant allele frequencies in domestic cats of Portugal and the Azores

The genetic profiles of cat populations of mainland Portugal are basically similar to those of the adjacent Atlantic littoral. The profiles of Azorean populations, while relatively homogeneous among themselves, are strikingly different from the mainland. It is tentatively concluded that some form of selective migration was the most important contributing factor in establishing the differences.     

Occurrence and Genetic Diversity of Uncultured Legionella spp. in Drinking Water Treated at Temperatures below 15°C

Representatives of the genus Legionella were detected by use of a real-time PCR method in all water samples collected directly after treatment from 16 surface water (SW) supplies prior to postdisinfection and from 81 groundwater (GW) supplies. Legionella concentrations ranged from 1.1 × 10³ to 7.8 × 10⁵ cells liter⁻¹ and were significantly higher in SW treated with multiple barriers at 4°C than in GW treated at 9 to 12°C with aeration and filtration but without chemical disinfection. No Legionellae (<50 CFU liter⁻¹) were detected in treated water by the culture method. Legionella was also observed in untreated SW and in untreated aerobic and anaerobic GW. Filtration processes in SW and GW treatment had little effect or increased the Legionella concentration, but ozonation in SW treatment caused about 1-log-unit reduction. A phylogenetic analysis of 16S rRNA gene sequences of 202 clones, obtained from a selection of samples, showed a high similarity (>91%) with Legionella sequences in the GenBank database. A total of 40 (33%) of the 16S rRNA gene sequences obtained from treated water were identified as described Legionella species and types, including L. bozemanii, L. worsleiensis, Legionella-like amoebal pathogen types, L. quateirensis, L. waltersii, and L. pneumophila. 16S rRNA gene sequences with a similarity of below 97% from described species were positioned all over the phylogenetic tree of Legionella. Hence, a large diversity of yet-uncultured Legionellae are common members of the microbial communities in SW and GW treated at water temperatures of below 15°C.