Temporal dynamics of co-circulating lineages of porcine reproductive and respiratory syndrome virus

Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) is the most important endemic pathogen in the U.S. swine industry. Despite control efforts involving improved biosecurity and different vaccination protocols, the virus continues to circulate and evolve. One of the foremost challenges in its control is high levels of genetic and antigenic diversity. Here, we quantify the co-circulation, emergence and sequential turnover of multiple PRRSV lineages in a single swine-producing region in the United States over a span of 9 years (2009–2017). By classifying over 4,000 PRRSV sequences (open-reading frame 5) into phylogenetic lineages and sub-lineages, we document the ongoing diversification and temporal dynamics of the PRRSV population, including the rapid emergence of a novel sub-lineage that appeared to be absent globally pre-2008. In addition, lineage 9 was the most prevalent lineage from 2009 to 2010, but its occurrence fell to 0.5% of all sequences identified per year after 2014, coinciding with the emergence or re-emergence of lineage 1 as the dominant lineage. The sequential dominance of different lineages, as well as three different sub-lineages within lineage 1, is consistent with the immune-mediated selection hypothesis for the sequential turnover in the dominant lineage. As host populations build immunity through natural infection or vaccination toward the most common variant, this dominant (sub-) lineage may be replaced by an emerging variant to which the population is more susceptible. An analysis of patterns of non- synonymous and synonymous mutations revealed evidence of positive selection on immunologically important regions of the genome, further supporting the potential that immune-mediated selection shapes the evolutionary and epidemiological dynamics for this virus. This has important implications for patterns of emergence and re-emergence of genetic variants of PRRSV that have negative impacts on the swine industry. Constant surveillance on PRRSV occurrence is crucial to a better understanding of the epidemiological and evolutionary dynamics of co-circulating viral lineages. Further studies utilizing whole genome sequencing and exploring the extent of cross-immunity between heterologous PRRS viruses could shed further light on PRRSV immunological response and aid in developing strategies that might be able to diminish disease impact

Infecção pelo complexo Mycobacterium tuberculosis em carneiro da Barbária (Ammotragus lervia) no Zoológico de Curitiba, sul do Brasil: relato de caso

A tuberculose é uma das doenças mundiais de notificação obrigatória mais importantes causada pelo complexo Mycobacterium tuberculosis que pode infectar pessoas e animais. A morte repentina de um carneiro da Barbária no Zoológico de Curitiba, que apresentou nódulos multifocais no pulmão à necropsia, levantou a suspeita de tuberculose. Foi realizada a Reação em Cadeia da Polimerase Quantitativa (qPCR) de fragmentos de órgãos e fluido. A qPCR detectou a presença do complexo M. tuberculosis nas amostras de pulmão. Este estudo relata a infecção pelo complexo M. tuberculosis no carneiro da Barbária, uma zoonose de grande relevância para a saúde pública, ressaltando-se a necessidade da implementação de medidas de prevenção. Além disso, pode prover um melhor entendimento sobre conservação de espécies, ocorrência e transmissão de doenças em cativeiro, potencial reservatório e impacto na saúde pública para visitantes e funcionários dos zoológicos.Tuberculosis is one of the most important mandatory notification diseases in the world caused by bacteria of the Mycobacterium tuberculosis complex, infecting both humans and animals. A sudden death of a Barbary sheep in Curitiba Zoo, and presence of multifocal nodules in lungs at necropsy raised suspicion of tuberculosis. Quantitative polymerase chain reaction (qPCR) from organs and fluid was performed and detected M. tuberculosis complex in a lung sample. This research reports the M. tuberculosis complex infection in Barbary sheep, a zoonosis of great relevance to public health and emphasizes the need to implement prevention measures. Furthermore, the research may provide a better understanding for species conservation, occurrence and transmission of diseases in captivity, reservoir potential and public health impact to zoo personnel and visitors.

História natural da leptospirose urbana: influência do sexo e da idade no risco de infecção, progressão clínica da doença e óbito

Submitted by Ana Maria Fiscina Sampaio ([email protected]) on 2013-10-18T16:50:09Z No. of bitstreams: 1 Igor Paploski Historia natural...2013.pdf: 1824673 bytes, checksum: 82176aba4d2b6446b2fb171b23ca4e2a (MD5)Made available in DSpace on 2013-10-18T16:50:09Z (GMT). No. of bitstreams: 1 Igor Paploski Historia natural...2013.pdf: 1824673 bytes, checksum: 82176aba4d2b6446b2fb171b23ca4e2a (MD5) Previous issue date: 2013Fundação Oswaldo Cruz. Centro de Pesquisas Gonçalo Moniz. Salvador, BA, BrasilLeptospirose é causada por bactérias do gênero Leptospira e é transmitida aos humanos pela urina de animais contaminados. Apenas uma parcela dos indivíduos infectados desenvolvem manifestações clínicas graves que requerem hospitalização e são potencialmente fatais. Os fatores que determinam que uma infecção por Leptospira evolua de forma autolimitada e outra progrida para uma doença grave e fatal ainda são pouco claros. Nós hipotetizamos que características demográficas como o sexo e a idade influenciem o risco de progressão clínica de indivíduos infectados pela Leptospira. OBJETIVO Investigar a influência do sexo e da idade no risco de progressão clínica da leptospirose após a infecção e estimar a razão entre o número de infecções subclínicas para cada caso grave e cada óbito por leptospirose em comunidades com alta transmissão da doença. MÉTODO Um estudo de coorte foi conduzido entre 2003 e 2006 para determinar a incidência de infecções subclínicas por Leptospira no bairro de Pau da Lima, uma comunidade carente de Salvador - BA . Paralelamente, pacientes com leptospirose grave e óbitos por leptospirose foram identificados através de vigilância populacional ativa no Hospital Couto Maia, em Salvador. Foi calculada a incidência de leptospirose grave e a mortalidade por leptospirose para áreas da cidade com características socioeconômicas similares a da área do estudo de coorte. Todas as incidências foram estratificadas por faixa etária e sexo, sendo em seguida comparadas através de razões de risco. RESULTADOS Foi identificada uma incidência média anual de 23,8 (IC 95%, 19,7 – 28,8) casos de infecção subclínica/1.000 habitantes na área da coorte. Em habitantes de áreas da cidade com características socioeconômicas similares a da área do estudo de coorte a incidência média anual de formas graves foi de 8,2 (IC 95%, 7,0 – 9,4) casos/100.000, sendo que a mortalidade por leptospirose média anual nesta população foi de 1,6 (IC 95%, 1,2 – 2,0) óbitos/100.000 habitantes. Homens apresentaram um risco 2,0 (IC 95%, 1,6 – 2,6) vezes maior de desenvolverem infecções subclínicas, 6,1 (IC 95%, 5,2 – 7,2) vezes maior de desenvolverem infecções graves e 0,6 (IC 95%, 0,4 – 1,0) vezes menor de evoluir para óbito do que mulheres. Indivíduos da faixa etária de 25 a 34 anos e de 35 a 44 anos de idade apresentaram um risco de desenvolverem infecções subclínicas 2,5 (IC 95%, 1,8 – 3,6) e 1,3 (IC 95%, 0,8 – 2,3) vezes maior, respectivamente, em comparação aos com idade entre 5 a 14 anos, enquanto que os indivíduos das mesmas faixas etárias apresentaram riscos de leptospirose grave de 4,5 (IC 95%, 2,2 – 9,0) e 5,1 (IC 95%, 2,5 – 10,3) vezes, respectivamente. Estima-se que ocorreram 289 e 1.510 infecções subclínicas para cada caso grave e para cada óbito, respectivamente, identificados e analisados neste estudo. CONCLUSÕES O sexo e a idade influenciam de risco de infecção subclínica, grave e de óbito por leptospirose. Homens tem maior risco de infecção subclínica e grave, entretanto mulheres apresentam maior letalidade de leptospirose. O risco para infecções subclínicas alcança o pico em indivíduos de 25 a 34 anos, entretanto o risco para infecções graves e óbito não se comporta da mesma maneira e aumenta com a idade.INTRODUCTION Leptospirosis is caused by a bacteria of the genus Leptospira and is transmited to humans by the urine of infected animals. Only a portion of infected individuals develop severe clinical manifestations that require hospitalization and are potentially fatal. The factors that determine if a Leptospira infection will evolve in a self-limiting while others will progress to a severe and fatal disease are still unclear. We hipothesize that demographic characteristics such as age and gender influence the risk of clinical progression of individuals infected with Leptospira. OBJECTIVE To investigate the influence of gender and age on the risk of clinical progression of leptospirosis after infection and estimate the infection to disease and infection to death ratio in communities with high disease transmission. METHODS A cohort study was performed between 2003 and 2006 to determine the incidence of subclinical infections of leptospirosis at Pau da Lima, a poor community of Salvador. In addition, patients with severe leptospirosis and deaths by leptospirosis were identified through active surveillance population at the infectious disease state reference hospital, in Salvador. We calculated the incidence of severe leptospirosis and mortality by leptospirosis in areas of the city with similar socioeconomic characteristics of the area of the cohort study. All incidences were stratified by age and sex, and then compared using risk ratios. RESULTS The mean annual incidence of subclinical infection was 23.8 (95% CI, 19.7 to 28.8) per 1,000 residents in the cohort area. The mean annual incidence of severe leptospirosis was 8.2 (95% CI, 7.0 – 9.4) cases per 100,000 inhabitants in areas with similar socioeconomic characteristics of the area of the cohort study. The mean annual mortality for individuals of the same area was 1.6 (95% CI, 1.2 – 2.0) per 100,000 inhabitants. Males have 2.0 (95% CI, 1.6 - 2.6) times the risk of developing subclinical infections, 6.1 (95% CI, 5.2 - 7.2) times the risk to develop severe infections and 0.6 (95% CI, 0.4 to 1.0) times the risk to evolve to death, compared to females. Individuals aged from 25 to 34 years and 35 to 44 years had a risk of developing subclinical leptospirosis 2.5 (95% CI , 1.8 - 3.6) and 1.3 (95% CI, 0,8 - 2.3) times greater, respectively, when compared to individuals aged 5 to 14 years, while individuals of the same age had a risk for severe leptospirosis 4.5 (95% CI, 2.2 - 9.0) and 5.1 (95% CI, 2.5 - 10.3) times greater, respectively. It is estimated that there were 1,510 and 289 subclinical infections for every death and severe leptospirosis cases, respectively, identified and analyzed in this study. CONCLUSIONS Age and gender influences the risk of subclinical and severe infection, and death from severe leptospirosis. Males have a higher risk of subclinical and severe infection, but females have higher lethality of leptospirosis. The risk for subclinical infection peaks in individuals aged 25 to 34 years, however, the risk for severe infection and death by leptospiris does not evolve in the same manner, increasing with age

Forecasting viral disease outbreaks at the farm-level for commercial sow farms in the US

Porcine epidemic diarrhea virus (PEDv) was introduced to the U.S. in 2013 and is now considered to be endemic. Like many endemic diseases, it is challenging for producers to estimate and respond to spatial and temporal variation in risk. Utilizing a regional spatio-temporal dataset containing weekly PEDv infection status for similar to 15 % of the U.S. sow herd, we present a machine learning platform developed to forecast the probability of PEDv infection in sow farms in the U.S. Participating stakeholders (swine production companies) in a swine-dense region of the U.S. shared weekly information on a) PEDv status of farms and b) animal movements for the past week and scheduled movements for the upcoming week. Environmental (average temperature, humidity, among others) and land use characteristics (hog density, proportion of area with different land uses) in a 5 km radius around each farm were summarized. Using the Extreme Gradient Boosting (XGBoost) machine learning model with Synthetic Minority Over-sampling Technique (SMOTE), we developed a near real-time tool that generates weekly PEDv predictions (pertaining to two-weeks in advance) to farms of participating stakeholders. Based on retrospective data collected between 2014 and 2017, the sensitivity, specificity, positive and negative predictive values of our model were 19.9, 99.9, 70.5 and 99.4 %, respectively. Overall accuracy was 99.3 %, although this metric is heavily biased by imbalance in the data (less than 0.7 % of farms had an outbreak each week). This platform has been used to deliver weekly real-time forecasts since December 2019. The forecast platform has a built-in feature to re-train the predictive model in order to remain as relevant as possible to current epidemiological situations, or to expand to a different disease. These dynamic forecasts, which account for recent animal movements, present disease distribution, and environmental factors, will promote data-informed and targeted disease management and prevention within the U.S. swine industry

Porcine reproductive and respiratory syndrome virus 2 (PRRSV-2) genetic diversity and occurrence of wild type and vaccine-like strains in the United States swine industry

Porcine reproductive and respiratory syndrome virus genotype 2 (PRRSV-2) genetic diversity in the U.S. was assessed using a database comprising 10 years' worth of sequence data obtained from swine production systems routine monitoring and outbreak investigations. A total of 26,831 ORF5 PRRSV-2 sequences from 34 production systems were included in this analysis. Within group mean genetic distance (i.e. mean proportion of nucleotide differences within ORF5) per year according to herd type was calculated for all PRRSV-2 sequences. The percent nucleotide difference between each sequence and the ORF5 sequences from four commercially available PRRSV-2 vaccines (Ingelvac PRRS MLV, Ingelvac PRRS ATP, Fostera PRRS, and Prevacent PRRS) within the same lineage over time was used to classify sequences in wild-type or vaccine-like. The mean ORF5 genetic distance fluctuated from 0.09 to 0.13, being generally smaller in years in which there was a relative higher frequency of dominant lineage. Vaccine-like sequences comprised about one fourth of sequences obtained through routine monitoring of PRRS. We found that lineage 5 sequences were mostly Ingelvac PRRS MLV-like. Lineage 8 sequences up to 2011 were 62.9% Ingelvac PRRS ATP-like while the remaining were wild-type viruses. From 2012 onwards, 51.9% of lineage 8 sequences were Ingelvac PRRS ATP-like, 45.0% were Fostera PRRS-like, and only 3.2% were wild-type. For lineage 1 sequences, 0.1% and 1.7% of the sequences were Prevacent PRRS-like in 2009-2018 and 2019, respectively. These results suggest that repeated introductions of vaccine-like viruses through use of modified live vaccines might decrease within-lineage viral diversity as vaccine-like strains become more prevalent. Overall, this compilation of private data from routine monitoring provides valuable information on PRRSV viral diversity

Storm drains as larval development and adult resting sites for Aedes aegypti and Aedes albopictus in Salvador, Brazil

Submitted by Ana Maria Fiscina Sampaio ([email protected]) on 2016-07-29T17:21:53Z No. of bitstreams: 1 Paploski IAD Storm drains as larval development and adult resting sites for Aedes aegypti and Aedes albopictus in Salvador, Brazil.pdf: 1792453 bytes, checksum: 44a287845c53ec88ae9185b031a21bd4 (MD5)Approved for entry into archive by Ana Maria Fiscina Sampaio ([email protected]) on 2016-07-29T17:35:25Z (GMT) No. of bitstreams: 1 Paploski IAD Storm drains as larval development and adult resting sites for Aedes aegypti and Aedes albopictus in Salvador, Brazil.pdf: 1792453 bytes, checksum: 44a287845c53ec88ae9185b031a21bd4 (MD5)Made available in DSpace on 2016-07-29T17:35:25Z (GMT). No. of bitstreams: 1 Paploski IAD Storm drains as larval development and adult resting sites for Aedes aegypti and Aedes albopictus in Salvador, Brazil.pdf: 1792453 bytes, checksum: 44a287845c53ec88ae9185b031a21bd4 (MD5) Previous issue date: 2016National Council for Scientific and Technological DevelopmentFundação Gonçalo Moniz. Centro de Pesquisas Gonçalo Moniz. Salvador, BA, Brasil / Universidade Federal da Bahia. Instituto de Saúde Coletiva. Salvador, BA, BrasilFundação Gonçalo Moniz. Centro de Pesquisas Gonçalo Moniz. Salvador, BA, Brasil / Universidade Federal da Bahia. Instituto de Saúde Coletiva. Salvador, BA, BrasilFundação Gonçalo Moniz. Centro de Pesquisas Gonçalo Moniz. Salvador, BA, Brasil / Universidade Federal da Bahia. Instituto de Saúde Coletiva. Salvador, BA, Brasil / Universidade Pedagógica de Quelimane. Quelimane, ZB, MozambiqueFundação Gonçalo Moniz. Centro de Pesquisas Gonçalo Moniz. Salvador, BA, Brasil / Universidade Federal da Bahia. Instituto de Saúde Coletiva. Salvador, BA, BrasilFundação Gonçalo Moniz. Centro de Pesquisas Gonçalo Moniz. Salvador, BA, BrasilFundação Gonçalo Moniz. Centro de Pesquisas Gonçalo Moniz. Salvador, BA, Brasil / Universidade Federal da Bahia. Faculdade de Medicina. Salvador, BA, BrasilFundação Gonçalo Moniz. Centro de Pesquisas Gonçalo Moniz. Salvador, BA, Brasil / Emory University. Atlanta, GE, USA.Fundação Gonçalo Moniz. Centro de Pesquisas Gonçalo Moniz. Salvador, BA, Brasil / Universidade Federal da Bahia. Instituto de Saúde Coletiva. Salvador, BA, BrasilDengue (DENV), Chikungunya (CHIKV), Zika (ZIKV), as well as yellow fever (YFV) viruses are transmitted to humans by Aedes spp. females. In Salvador, the largest urban center in north-eastern Brazil, the four DENV types have been circulating, and more recently, CHIKV and ZIKV have also become common. We studied the role of storm drains as Aedes larval development and adult resting sites in four neighbourhoods of Salvador, representing different socioeconomic, infrastructure and topographic conditions. Results: A sample of 122 storm drains in the four study sites were surveyed twice during a 4-month period in 2015; in 49.0 % of the visits, the storm drains contained water. Adults and immatures of Aedes aegypti were captured in two of the four sites, and adults and immatures of Aedes albopictus were captured in one of these two sites. A total of 468 specimens were collected: 148 Ae. aegypti (38 adults and 110 immatures), 79 Ae. albopictus (48 adults and 31 immatures), and 241 non-Aedes (mainly Culex spp.) mosquitoes (42 adults and 199 immatures). The presence of adults or immatures of Ae. aegypti in storm drains was independently associated with the presence of non-Aedes mosquitoes and with rainfall of 50 mm during the preceding week. Conclusions: We found that in Salvador, one of the epicentres of the 2015 ZIKV outbreak, storm drains often accumulate water and serve as larval development sites and adult resting areas for both Ae. aegypti and Ae. albopictus. Vector control campaigns usually overlook storm drains, as most of the effort to prevent Ae. agypti reproduction is directed towards containers in the domicile environment. While further studies are needed to determine the added contribution of storm drains for the maintenance of Aedes spp. populations, we advocate that vector control programs incorporate actions directed at storm drains, including regular inspections and use of larvicides, and that human and capital resources are mobilized to modify storm drains, so that they do not serves as larval development sites for Aedes (and other) mosquitoes

Congenital brain abnormalities during a Zika virus epidemic in Salvador, Brazil, April 2015 to July 2016

Submitted by Ana Maria Fiscina Sampaio ([email protected]) on 2019-02-01T12:59:05Z No. of bitstreams: 1 KIKUTI, M. Congenital brain abnormalitie...2018.pdf: 206258 bytes, checksum: 3991c4208908ad82ee462e12781815f7 (MD5)Approved for entry into archive by Ana Maria Fiscina Sampaio ([email protected]) on 2019-02-01T13:32:55Z (GMT) No. of bitstreams: 1 KIKUTI, M. Congenital brain abnormalitie...2018.pdf: 206258 bytes, checksum: 3991c4208908ad82ee462e12781815f7 (MD5)Made available in DSpace on 2019-02-01T13:32:55Z (GMT). No. of bitstreams: 1 KIKUTI, M. Congenital brain abnormalitie...2018.pdf: 206258 bytes, checksum: 3991c4208908ad82ee462e12781815f7 (MD5) Previous issue date: 2018The Brazilian National Council of Technological and Scientific Development, the Brazilian Coordination for the Improvement of Higher Education, the Bahia Foundation for Research Support, the National Institute of Neurological Disease and Stroke, the Manton Center for Orphan Disease Research, Boston Children’s Hospital Faculty Career Development Award and the David Rockefeller Center for Latin American Studies at Harvard University.Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Salvador, BA, Brasil / Universidade Federal da Bahia. Salvador, BA, Brasil.Secretaria Municipal de Saúde de Salvador. Salvador, BA, Brasil.Secretaria Municipal de Saúde de Salvador. Salvador, BA, Brasil.Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Salvador, BA, Brasil / Universidade Federal da Bahia. Salvador, BA, Brasil.Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Salvador, BA, Brasil / Emory University. Atlanta, United States.Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Salvador, BA, Brasil / Universidade Federal da Bahia. Salvador, BA, Brasil.Boston Children’s Hospital. Boston, United States / Massachusetts General Hospital. Boston, United States / Harvard Medical School. Boston, United States.Fundação Oswaldo Cruz. Instituto Gonçalo Moniz. Salvador, BA, Brasil / Universidade Federal da Bahia. Salvador, BA, Brasil.North-eastern Brazil was the region most affected by the outbreak of congenital Zika syndrome that followed the 2015 Zika virus (ZIKV) epidemics, with thousands of suspected microcephaly cases reported to the health authorities, mostly between late 2015 and early 2016. Aim: To describe clinical and epidemiological aspects of the outbreak of congenital brain abnormalities (CBAs) and to evaluate the accuracy of different head circumference screening criteria in predicting CBAs. Method: Between April 2015 and July 2016, the Centers for Information and Epidemiologic Surveillance of Salvador, Brazil investigated the reported cases suspected of microcephaly and, based on intracranial imaging studies, confirmed or excluded a diagnosis of CBA. Sensitivity, specificity and positive and negative predictive values of different head circumference screening criteria in predicting CBAs were calculated. Results: Of the 365 investigated cases, 166 (45.5%) had confirmed CBAs. The most common findings were intracranial calcifications and ventriculomegaly in 143 (86.1%) and 111 (66.9%) of the 166 CBA cases, respectively. Prevalence of CBAs peaked in December 2015 (2.24 cases/100 live births). Cases of CBAs were significantly more likely to have been born preterm and to mothers who had clinical manifestations of arboviral infection during pregnancy. None of the head circumference screening criteria performed optimally in predicting CBAs. Conclusion: This study highlights the magnitude of neurological consequences of the ZIKV epidemic and the limitations of head circumference in accurately identifying children with CBA. Gestational symptoms compatible with ZIKV infection should be combined with imaging studies for efficient detection of suspect CBAs during ZIKV epidemics

Seroprevalence and seroincidence of Leptospira infection in dogs during a one-year period in an endemic urban area in Southern Brazil

Introduction: Leptospirosis is a zoonosis that affects both humans and animals. Dogs may serve as sentinels and indicators of environmental contamination as well as potential carriers for Leptospira. This study aimed to evaluate the seroprevalence and seroincidence of leptospirosis infection in dogs in an urban low-income community in southern Brazil where human leptospirosis is endemic. Methods: A prospective cohort study was designed that consisted of sampling at recruitment and four consecutive trimestral follow-up sampling trials. All households in the area were visited, and those that owned dogs were invited to participate in the study. The seroprevalence (MAT titers >= 100) of Leptospira infection in dogs was calculated for each visit, the seroincidence (seroconversion or four-fold increase in serogroup-specific MAT titer) density rate was calculated for each follow-up, and a global seroincidence density rate was calculated for the overall period. Results: A total of 378 dogs and 902.7 dog-trimesters were recruited and followed, respectively. The seroprevalence of infection ranged from 9.3% (95% CI; 6.7 - 12.6) to 19% (14.1 - 25.2), the seroincidence density rate of infection ranged from 6% (3.3 - 10.6) to 15.3% (10.8 - 21.2), and the global seroincidence density rate of infection was 11% (9.1 - 13.2) per dog-trimester. Canicola and Icterohaemorraghiae were the most frequent incident serogroups observed in all follow-ups. Conclusions: Follow-ups with mean trimester intervals were incapable of detecting any increase in seroprevalence due to seroincident cases of canine leptospirosis, suggesting that antibody titers may fall within three months. Further studies on incident infections, disease burden or risk factors for incident Leptospira cases should take into account the detectable lifespan of the antibody