Dogs and Opossums Positive for Vaccinia Virus during Outbreak Affecting Cattle and Humans, Sao Paulo State, Brazil.
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ABSTRACT:
SUBMITTER: Peres MG
PROVIDER: S-EPMC4734541 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundDengue studies at the urban scale are scarce and required for guiding control efforts. In Brazil, the burden of dengue is high and challenges city public health administrations with limited resources. Here we studied the dynamics of a dengue epidemic in a single city.MethodsSerum samples from dengue suspected cases were collected and tested, from December 2012 and July 2013 in Guarujá, Brazil. We use incidence series analysis to provide a detailed view of the reproduction number dynamics and a Bayesian analysis to infer the spread of the serotype using geographic and temporal data.ResultsWe obtained nucleotide sequences from 354 envelope genes and georeferenced 286 samples during the course of the outbreak. Serotype 4 was responsible for the epidemic. We identified at least two major lineages that overlapped in distribution. We observed high reproduction numbers and high cladogenesis prior to the escalation of clinical case notifications. Three densely populated non-adjacent neighborhoods played a pivotal role during the onset and/or course of the epidemic.DiscussionOur findings point to high dengue virus transmission with a substantial proportion of unapparent cases that led to a late recognition of an outbreak. Usually source reductions initiatives tend to be insufficient once an epidemic has been established. Nevertheless, health authorities in Guarujá prioritized vector control on specific places with clusters of georeferenced viremic patients, which appear to have diminished the epidemic impact.
| S-EPMC4824887 | biostudies-literature
Project description:During a resurgence of measles in São Paulo, Brazil, in 1997, >40,000 cases (peak incidence rate of 246/100,000 inhabitants) and 42 measles-related deaths were reported. Reverse transcriptase-polymerase chain reaction and nucleotide sequencing were used to analyze specimens from patients who had typical clinical measles infection during this outbreak and from six patients who had had measles in 1995 and 1996. Although wild-type measles viruses (genotypes D5 and D6) were present in São Paulo before this resurgence, we detected only D6 viruses. The genotype D6 viruses isolated during this outbreak had identical sequences to genotype D6 viruses isolated in other parts of Brazil and South America in 1997 and 1998, suggesting that a single chain of transmission was responsible. We also identified genotype A viruses in two vaccine-associated cases from 1995 and 1996. Our findings extend the knowledge of the circulation patterns of measles virus in South America, contributing to measles control efforts in the Americas.
| S-EPMC2732519 | biostudies-literature
Project description:The dengue virus has a single-stranded positive-sense RNA genome of approximately 10.700 nucleotides with a single open reading frame that encodes three structural (C, prM, and E) and seven nonstructural (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5) proteins. It possesses four antigenically distinct serotypes (DENV 1-4). Many phylogenetic studies address particularities of the different serotypes using convenience samples that are not conducive to a spatio-temporal analysis in a single urban setting. We describe the pattern of spread of distinct lineages of DENV-3 circulating in São José do Rio Preto, Brazil, during 2006. Blood samples from patients presenting dengue-like symptoms were collected for DENV testing. We performed M-N-PCR using primers based on NS5 for virus detection and identification. The fragments were purified from PCR mixtures and sequenced. The positive dengue cases were geo-coded. To type the sequenced samples, 52 reference sequences were aligned. The dataset generated was used for iterative phylogenetic reconstruction with the maximum likelihood criterion. The best demographic model, the rate of growth, rate of evolutionary change, and Time to Most Recent Common Ancestor (TMRCA) were estimated. The basic reproductive rate during the epidemics was estimated. We obtained sequences from 82 patients among 174 blood samples. We were able to geo-code 46 sequences. The alignment generated a 399-nucleotide-long dataset with 134 taxa. The phylogenetic analysis indicated that all samples were of DENV-3 and related to strains circulating on the isle of Martinique in 2000-2001. Sixty DENV-3 from São José do Rio Preto formed a monophyletic group (lineage 1), closely related to the remaining 22 isolates (lineage 2). We assumed that these lineages appeared before 2006 in different occasions. By transforming the inferred exponential growth rates into the basic reproductive rate, we obtained values for lineage 1 of R(0) = 1.53 and values for lineage 2 of R(0) = 1.13. Under the exponential model, TMRCA of lineage 1 dated 1 year and lineage 2 dated 3.4 years before the last sampling. The possibility of inferring the spatio-temporal dynamics from genetic data has been generally little explored, and it may shed light on DENV circulation. The use of both geographic and temporally structured phylogenetic data provided a detailed view on the spread of at least two dengue viral strains in a populated urban area.
| S-EPMC2682200 | biostudies-literature
Project description:To estimate the prevalence of one month psychotropic drug use in São Paulo, Brazil, and to assess the gap treatment between the presence of mental disorders and psychotropic drug users.A probabilistic sample of non-institutionalized individuals from the general population of São Paulo (n = 2336; turnout: 84.5%) who were 15 years or older were interviewed by a trained research staff, applying the Composite International Diagnostic Interview 2.1 (CIDI WHO) (depression, anxiety-phobia, OCD\PTSD, alcoholism sections), and an inventory investigating psychotropic drug use during the 12-month and one-month periods immediately preceding the interview. Logistic models were fitted to investigate associations between psychotropic drug use as well as socio-demographic and clinical variables.The one month prevalence of psychotropic drug use in São Paulo was 5.89%, the most commonly used drugs were antidepressants (3.15%) and tranquilizers (2.67%). A higher consumption of psychotropic drugs (overall, antidepressants and tranquilizers) was observed among women (OR:2.42), older individuals (OR:1.04), individuals with higher levels of formal education (1.06), and individuals with a family (OR:2.29) or personal history of mental illness (OR:3.27). The main psychotropic drug prescribers were psychiatrists (41%), followed by general practitioners (30%); 60% of psychotropic drugs were obtained through a government-run dispensing program. Most individuals who obtained a positive diagnosis on the CIDI 2.1 during the previous month were not using psychotropic medication (85%). Among individuals with a diagnosis of moderate to severe depression, 67.5% were not on any pharmacological treatment.There is a change in the type of psychotropic more often used in São Paulo, from benzodiazepines to antidepressants, this event is observed in different cultures. The prevalence of use is similar to other developing countries. Most of the patients presenting a psychiatric illness in the month prior to testing were not receiving any sort of psychiatric medication. This may be explained by a failure to identify cases in primary care, which could be improved (and access to treatment could be facilitated) if professionals received more specialized training in managing cases with mental health problems.
| S-EPMC4529275 | biostudies-other
Project description:IntroductionHand, foot, and mouth disease (HFMD) is an acute febrile illness characterized by fever; sore throat; and vesicular eruptions on the hands, feet, and oral mucosa. Outbreaks of HFMD in children aged <5 years have been reported worldwide and the major causative agents are Coxsackievirus (CV)A16, enterovirus (EV)-A71 and recently CVA6.Aim and methodsThe aim of this study was to investigated a large outbreak of Hand, foot, and mouth disease during COVID-19 pandemic in 2021 from clinical samples of 315 suspected cases, in São Paulo State, Brazil. Diagnostic evaluation was performed by RT-qPCR, culture cell isolation and serological neutralization assay. EV-positive were genotyped by partial VP1 genome sequencing.ResultsOne hundred and forty-nine cases analyzed were positive for enterovirus (47.3%; n = 149/315) by neutralizing test (n = 10 patients) and RT-qPCR (n = 139 patients), and identified as CVA6 sub-lineage D3 by analysis of VP1 partial sequences.ConclusionsThis finding indicated the reemergence of CVA6 in HFMD, soon after the gradual easing of non-pharmaceutical interventions during-pandemic COVID-19 and the relevance of continued surveillance of circulating enterovirus types in the post-COVID pandemic era.
| S-EPMC9301960 | biostudies-literature
Project description:The Hepeviridae comprise single-stranded positive-sense RNA viruses classified into two genera, Orthohepevirus and Piscihepevirus. Orthohepeviruses have a wide host range that includes rodents, but previous studies had been restricted to rodents of the Muridae family. In this study, we applied a high-throughput sequencing approach to examine the presence of orthohepeviruses in rodents from São Paulo State, Brazil. We also used RT-PCR to determine the frequency of orthohepeviruses in our sampled population. We identified novel orthohepeviruses in blood samples derived from Necromys lasiurus (1.19%) and Calomys tener (3.66%). Therefore, our results expand the host range and viral diversity of the Hepeviridae family.
| S-EPMC5998382 | biostudies-literature
Project description:Dengue virus (DENV) is an arbovirus belonging to the genus Flavivirus, family Flaviviridae In Brazil, the reemergence and spread of DENV type 4 (DENV-4) across the country were responsible for a significant outbreak in Guarujá, São Paulo, Brazil. Here, we report the first genomic sequences of DENV strains circulating in Guarujá during the 2013 outbreak.
| S-EPMC5511897 | biostudies-literature
Project description:Norovirus (NoV), previously called Norwalk-like virus, represents an important group of human pathogens associated with outbreaks of nonbacterial gastroenteritis. Epidemiological surveys of outbreaks have shown that the most important routes of transmission are person-to-person contacts and contaminated food and water, with the virus affecting adults and children. NoV is classified into genogroups, being genogroups GI, GII and GIV found in humans. In view of the high genetic diversity of NoV and the lack of information about this virus in Brazil, the aim of the present study was the molecular characterization of NoV isolated from diarrheic stool samples of patients from São Paulo State. In this study, 204 stool specimens collected during diarrhea outbreaks were analyzed by RT-PCR, and 12 were sequenced for genogroup confirmation. One-step PCR was performed in order to amplify the B region of ORF 1 using the MON 431, 432, 433 and 434 primer pool. From total, 32 (15.7%) stool specimens were positive for NoV genogroup GII. Comparison of the sequences of the PCR products to GenBank sequences showed 88.8% to 98.8% identity, suggesting the presence of genogroup GII in gastroenteritis outbreaks in São Paulo State.
| S-EPMC3768465 | biostudies-literature
Project description:The objective of this study was to characterize the prevalence of viral encephalitis due to arbovirus infection of the Togaviridae and Flaviviridae families in São Paulo, Brazil. A total of 500 cerebrospinal fluid (CSF) samples collected between August 2012 and January 2013, from patients with symptoms of acute encephalitis were analyzed. Findings suggestive of viral encephalitis-elevations in cell concentration, glucose and total protein-were observed in 234 (46.8%) samples, designated as Group 1. The remaining 266 samples comprised Group 2. All samples were tested for Flaviviruses (dengue virus 1, 2, 3 and 4, yellow fever virus and West Nile virus), Alphavirus (NS5 region) and enterovirus by RT- PCR and for herpesviruses and enteroviruses using CLART-Entherpex. A presumptive viral etiological agent was detected in 26 samples (5.2%), 18 (8.0%) in Group 1 and 8 (3.0%) in Group 2. In Group 1 human herpesviruses were detected in 9 cases, enteroviruses in 7 cases, dengue viruses (DENV) in 2 CSFs and St. Louis encephalitis virus (SLEV) in one case. In Group 2 there were 3 CSFs positive for human herpesviruses, 2 for enteroviruses, 2 for DENV and 1 for SLEV. Detection of arboviruses, even though present in a minority of infected patients, identifies these viruses as a probable etiological agent of encephalitis. This is of special concern in regions where this class of viruses is endemic and has been linked to other recent epidemics.
| S-EPMC6331147 | biostudies-literature
Project description:Roadkill estimates for different species and species groups are available for many countries and regions. However, there is a lack of information from tropical countries, including from Latin America. In this study, we analyzed medium and large-sized mammal roadkill data from 18 toll road companies (TRC) in São Paulo State (6,580 km of monitored toll roads), Brazil. We extrapolated these roadkill numbers to the entire system of major paved roads in the State (36,503 km). The TRC collected mammal-road- mortality data both before (2-lanes) and after (4-lanes) road reconstruction. We used the "before" data from the TRC to estimate annual mammal-road-mortality along 2-lane roads that remained public roads. Combined with the data for the new 4-lane highways, this allowed us to estimate annual mammal road mortality for all the paved roads in the State. During 10 years of roadkill monitoring along toll roads, a total of 37,744 roadkilled mammals were recorded, representing a total of 32 medium to large-sized mammal species (average number of roadkilled individuals/year = 3,774 ± 1,159; min = 1,932; max = 5,369; 0.6 individuals roadkilled/km/year). Most roadkilled species were common generalists, but there were also relatively high roadkill numbers of threatened and endangered species (4.3% of the data), which is a serious conservation concern. Most of the roadkill was reported occurred during the nocturnal period (66%, n = 14,189) and in the rainy months (October-March) (55%, n = 15,318). Reported mammal roadkill tended to increase between 2009 and 2014 (R2 = 0.614; p = 0.065), with an average increase of 313.5 individuals/year. Extrapolation of the results to the entire São Paulo State, resulted in an average estimate of 39,605 medium and large-sized mammals roadkilled per year. Our estimates of the number of roadkilled individuals can be used as one of the input parameters in population viability analyses to understand the extinction or extirpation risk, especially for threatened and endangered species.
| S-EPMC7846925 | biostudies-literature