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1.
Mol Biol Evol ; 41(1)2024 Jan 03.
Artigo em Inglês | MEDLINE | ID: mdl-38158742

RESUMO

Sequencing of viral infections has become increasingly common over the last decade. Deep sequencing data in particular have proven useful in characterizing the roles that genetic drift and natural selection play in shaping within-host viral populations. They have also been used to estimate transmission bottleneck sizes from identified donor-recipient pairs. These bottleneck sizes quantify the number of viral particles that establish genetic lineages in the recipient host and are important to estimate due to their impact on viral evolution. Current approaches for estimating bottleneck sizes exclusively consider the subset of viral sites that are observed as polymorphic in the donor individual. However, these approaches have the potential to substantially underestimate true transmission bottleneck sizes. Here, we present a new statistical approach for instead estimating bottleneck sizes using patterns of viral genetic variation that arise de novo within a recipient individual. Specifically, our approach makes use of the number of clonal viral variants observed in a transmission pair, defined as the number of viral sites that are monomorphic in both the donor and the recipient but carry different alleles. We first test our approach on a simulated dataset and then apply it to both influenza A virus sequence data and SARS-CoV-2 sequence data from identified transmission pairs. Our results confirm the existence of extremely tight transmission bottlenecks for these 2 respiratory viruses.


Assuntos
Deriva Genética , Vírus da Influenza A , Vírus da Influenza A/genética , Seleção Genética , Variação Genética
2.
J Virol ; 98(1): e0161823, 2024 Jan 23.
Artigo em Inglês | MEDLINE | ID: mdl-38174928

RESUMO

The global evolution of SARS-CoV-2 depends in part upon the evolutionary dynamics within individual hosts with varying immune histories. To characterize the within-host evolution of acute SARS-CoV-2 infection, we sequenced saliva and nasal samples collected daily from vaccinated and unvaccinated individuals early during infection. We show that longitudinal sampling facilitates high-confidence genetic variant detection and reveals evolutionary dynamics missed by less-frequent sampling strategies. Within-host dynamics in both unvaccinated and vaccinated individuals appeared largely stochastic; however, in rare cases, minor genetic variants emerged to frequencies sufficient for forward transmission. Finally, we detected significant genetic compartmentalization of viral variants between saliva and nasal swab sample sites in many individuals. Altogether, these data provide a high-resolution profile of within-host SARS-CoV-2 evolutionary dynamics.IMPORTANCEWe detail the within-host evolutionary dynamics of SARS-CoV-2 during acute infection in 31 individuals using daily longitudinal sampling. We characterized patterns of mutational accumulation for unvaccinated and vaccinated individuals, and observed that temporal variant dynamics in both groups were largely stochastic. Comparison of paired nasal and saliva samples also revealed significant genetic compartmentalization between tissue environments in multiple individuals. Our results demonstrate how selection, genetic drift, and spatial compartmentalization all play important roles in shaping the within-host evolution of SARS-CoV-2 populations during acute infection.


Assuntos
Evolução Molecular , Deriva Genética , SARS-CoV-2 , Humanos , COVID-19/virologia , Nariz/virologia , Saliva/virologia , SARS-CoV-2/genética , Masculino , Feminino , Adolescente , Adulto Jovem , Adulto , Pessoa de Meia-Idade
3.
Arch Womens Ment Health ; 22(4): 467-473, 2019 08.
Artigo em Inglês | MEDLINE | ID: mdl-30251209

RESUMO

The perinatal period is a critical time for mental health and is also associated with high health care expenditure. Our previous work has identified a history of poor mental health as the strongest predictor of poor perinatal mental health. This study aims to examine the impact of a history of poor mental health on health care costs during the perinatal period. Data from the 1973-1978 cohort of the Australian Longitudinal Study on Women's Health (ALSWH) were linked with a number of administrative datasets including the NSW Admitted Patient Data Collection and Perinatal Data Collection, the Medicare Benefits Scheme and the Pharmaceuticals Benefits Scheme between 2002 and 2011. Even when taking birth type and private health insurance status into account, a history of poor mental health resulted in an average increase of over 11% per birth across the perinatal period. These findings indicate that an investment in prevention and early treatment of poor mental health prior to child bearing may result in a cost saving in the perinatal period and a reduction of the incidence of women experiencing poor perinatal mental health.


Assuntos
Ansiedade/terapia , Depressão/terapia , Custos de Cuidados de Saúde/estatística & dados numéricos , Transtornos Mentais/terapia , Serviços de Saúde Mental/economia , Assistência Perinatal/economia , Adulto , Ansiedade/diagnóstico , Ansiedade/economia , Austrália , Depressão/diagnóstico , Depressão/economia , Feminino , Humanos , Recém-Nascido , Estudos Longitudinais , Bem-Estar Materno , Transtornos Mentais/economia , Saúde Mental , Serviços de Saúde Mental/estatística & dados numéricos , Assistência Perinatal/métodos , Período Pós-Parto , Gravidez , Estados Unidos , Saúde da Mulher
4.
Proc Natl Acad Sci U S A ; 112(42): 12997-3002, 2015 Oct 20.
Artigo em Inglês | MEDLINE | ID: mdl-26417090

RESUMO

Cold-water conditions have excluded durophagous (skeleton-breaking) predators from the Antarctic seafloor for millions of years. Rapidly warming seas off the western Antarctic Peninsula could now facilitate their return to the continental shelf, with profound consequences for the endemic fauna. Among the likely first arrivals are king crabs (Lithodidae), which were discovered recently on the adjacent continental slope. During the austral summer of 2010 ‒ 2011, we used underwater imagery to survey a slope-dwelling population of the lithodid Paralomis birsteini off Marguerite Bay, western Antarctic Peninsula for environmental or trophic impediments to shoreward expansion. The population density averaged ∼ 4.5 individuals × 1,000 m(-2) within a depth range of 1,100 ‒ 1,500 m (overall observed depth range 841-2,266 m). Images of juveniles, discarded molts, and precopulatory behavior, as well as gravid females in a trapping study, suggested a reproductively viable population on the slope. At the time of the survey, there was no thermal barrier to prevent the lithodids from expanding upward and emerging on the outer shelf (400- to 550-m depth); however, near-surface temperatures remained too cold for them to survive in inner-shelf and coastal environments (<200 m). Ambient salinity, composition of the substrate, and the depth distribution of potential predators likewise indicated no barriers to expansion of lithodids onto the outer shelf. Primary food resources for lithodids--echinoderms and mollusks--were abundant on the upper slope (550-800 m) and outer shelf. As sea temperatures continue to rise, lithodids will likely play an increasingly important role in the trophic structure of subtidal communities closer to shore.


Assuntos
Crustáceos/fisiologia , Animais , Regiões Antárticas , Mudança Climática , Feminino , Masculino , Dinâmica Populacional , Comportamento Sexual Animal
5.
Virus Evol ; 10(1): veae042, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38883977

RESUMO

Influenza infections result in considerable public health and economic impacts each year. One of the contributing factors to the high annual incidence of human influenza is the virus's ability to evade acquired immunity through continual antigenic evolution. Understanding the evolutionary forces that act within and between hosts is therefore critical to interpreting past trends in influenza virus evolution and in predicting future ones. Several studies have analyzed longitudinal patterns of influenza A virus genetic diversity in natural human infections to assess the relative contributions of selection and genetic drift on within-host evolution. However, in these natural infections, within-host viral populations harbor very few single-nucleotide variants, limiting our resolution in understanding the forces acting on these populations in vivo. Furthermore, low levels of within-host viral genetic diversity limit the ability to infer the extent of drift across transmission events. Here, we propose to use influenza virus genomic diversity as an alternative signal to better understand within- and between-host patterns of viral evolution. Specifically, we focus on the dynamics of defective viral genomes (DVGs), which harbor large internal deletions in one or more of influenza virus's eight gene segments. Our longitudinal analyses of DVGs show that influenza A virus populations are highly dynamic within hosts, corroborating previous findings based on viral genetic diversity that point toward the importance of genetic drift in driving within-host viral evolution. Furthermore, our analysis of DVG populations across transmission pairs indicates that DVGs rarely appeared to be shared, indicating the presence of tight transmission bottlenecks. Our analyses demonstrate that viral genomic diversity can be used to complement analyses based on viral genetic diversity to reveal processes that drive viral evolution within and between hosts.

6.
medRxiv ; 2024 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-38558994

RESUMO

HIV incidence has been declining in Africa with scale-up of HIV interventions. However, there is limited data on HIV evolutionary trends in African populations with waning epidemics. We evaluated changes in HIV viral diversity and genetic divergence in southern Uganda over a twenty-five-year period spanning the introduction and scale-up of HIV prevention and treatment programs using HIV sequence and survey data from the Rakai Community Cohort Study, an open longitudinal population-based HIV surveillance cohort. Gag (p24) and env (gp41) HIV data were generated from persons living with HIV (PLHIV) in 31 inland semi-urban trading and agrarian communities (1994 to 2018) and four hyperendemic Lake Victoria fishing communities (2011 to 2018) under continuous surveillance. HIV subtype was assigned using the Recombination Identification Program with phylogenetic confirmation. Inter-subtype diversity was estimated using the Shannon diversity index and intra-subtype diversity with the nucleotide diversity and pairwise TN93 genetic distance. Genetic divergence was measured using root-to-tip distance and pairwise TN93 genetic distance analyses. Evolutionary dynamics were assessed among demographic and behavioral sub-groups, including by migration status. 9,931 HIV sequences were available from 4,999 PLHIV, including 3,060 and 1,939 persons residing in inland and fishing communities, respectively. In inland communities, subtype A1 viruses proportionately increased from 14.3% in 1995 to 25.9% in 2017 (p<0.001), while those of subtype D declined from 73.2% in 1995 to 28.2% in 2017 (p<0.001). The proportion of viruses classified as recombinants significantly increased by more than four-fold. Inter-subtype HIV diversity has generally increased. While p24 intra-subtype genetic diversity and divergence leveled off after 2014, diversity and divergence of gp41 increased through 2017. Inter- and intra-subtype viral diversity increased across all population sub-groups, including among individuals with no recent migration history or extra-community sexual partners. This study provides insights into population-level HIV evolutionary dynamics in declining African HIV epidemics following the scale-up of HIV prevention and treatment programs. Continued molecular surveillance may provide a better understanding of the dynamics driving population HIV evolution and yield important insights for epidemic control and vaccine development.

7.
Nat Commun ; 14(1): 3105, 2023 05 29.
Artigo em Inglês | MEDLINE | ID: mdl-37248255

RESUMO

Epidemiological models are commonly fit to case and pathogen sequence data to estimate parameters and to infer unobserved disease dynamics. Here, we present an inference approach based on sequence data that is well suited for model fitting early on during the expansion of a viral lineage. Our approach relies on a trajectory of segregating sites to infer epidemiological parameters within a Sequential Monte Carlo framework. Using simulated data, we first show that our approach accurately recovers key epidemiological quantities under a single-introduction scenario. We then apply our approach to SARS-CoV-2 sequence data from France, estimating a basic reproduction number of approximately 2.3-2.7 under an epidemiological model that allows for multiple introductions. Our approach presented here indicates that inference approaches that rely on simple population genetic summary statistics can be informative of epidemiological parameters and can be used for reconstructing infectious disease dynamics during the early expansion of a viral lineage.


Assuntos
COVID-19 , Doenças Transmissíveis , Vírus , Humanos , COVID-19/epidemiologia , SARS-CoV-2/genética , Vírus/genética , Número Básico de Reprodução , Teorema de Bayes
8.
bioRxiv ; 2023 Aug 14.
Artigo em Inglês | MEDLINE | ID: mdl-37645981

RESUMO

Sequencing of viral infections has become increasingly common over the last decade. Deep sequencing data in particular have proven useful in characterizing the roles that genetic drift and natural selection play in shaping within-host viral populations. They have also been used to estimate transmission bottleneck sizes from identified donor-recipient pairs. These bottleneck sizes quantify the number of viral particles that establish genetic lineages in the recipient host and are important to estimate due to their impact on viral evolution. Current approaches for estimating bottleneck sizes exclusively consider the subset of viral sites that are observed as polymorphic in the donor individual. However, allele frequencies can change dramatically over the course of an individual's infection, such that sites that are polymorphic in the donor at the time of transmission may not be polymorphic in the donor at the time of sampling and allele frequencies at donor-polymorphic sites may change dramatically over the course of a recipient's infection. Because of this, transmission bottleneck sizes estimated using allele frequencies observed at a donor's polymorphic sites may be considerable underestimates of true bottleneck sizes. Here, we present a new statistical approach for instead estimating bottleneck sizes using patterns of viral genetic variation that arose de novo within a recipient individual. Specifically, our approach makes use of the number of clonal viral variants observed in a transmission pair, defined as the number of viral sites that are monomorphic in both the donor and the recipient but carry different alleles. We first test our approach on a simulated dataset and then apply it to both influenza A virus sequence data and SARS-CoV-2 sequence data from identified transmission pairs. Our results confirm the existence of extremely tight transmission bottlenecks for these two respiratory viruses, using an approach that does not tend to underestimate transmission bottleneck sizes.

9.
Front Cell Infect Microbiol ; 13: 1081070, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36761897

RESUMO

Introduction: USA300 has remained the dominant community and healthcare associated methicillin-resistant Staphylococcus aureus (MRSA) clone in the United States and in northern South America for at least the past 20 years. In this time, it has experienced epidemic spread in both of these locations. However, its pre-epidemic evolutionary history and origins are incompletely understood. Large sequencing databases, such as NCBI, PATRIC, and Staphopia, contain clues to the early evolution of USA300 in the form of sequenced genomes of USA300 isolates that are representative of lineages that diverged prior to the establishment of the South American epidemic (SAE) clade and North American epidemic (NAE) clade. In addition, historical isolates collected prior to the emergence of epidemics can help reconstruct early events in the history of this lineage. Methods: Here, we take advantage of the accrued, publicly available data, as well as two newly sequenced pre-epidemic historical isolates from 1996, and a very early diverging ACME-negative NAE genome, to understand the pre-epidemic evolution of USA300. We use database mining techniques to emphasize genomes similar to pre-epidemic isolates, with the goal of reconstructing the early molecular evolution of the USA300 lineage. Results: Phylogenetic analysis with these genomes confirms that the NAE and SAE USA300 lineages diverged from a most recent common ancestor around 1970 with high confidence, and it also pinpoints the independent acquisition events of the of the ACME and COMER loci with greater precision than in previous studies. We provide evidence for a North American origin of the USA300 lineage and identify multiple introductions of USA300 into South and North America. Notably, we describe a third major USA300 clade (the pre-epidemic branching clade; PEB1) consisting of both MSSA and MRSA isolates circulating around the world that diverged from the USA300 lineage prior to the establishment of the South and North American epidemics. We present a detailed analysis of specific sequence characteristics of each of the major clades, and present diagnostic positions that can be used to classify new genomes.


Assuntos
Epidemias , Staphylococcus aureus Resistente à Meticilina , Infecções Estafilocócicas , Estados Unidos , Humanos , Filogenia , Infecções Estafilocócicas/epidemiologia , Genoma Bacteriano , Evolução Molecular
10.
Science ; 375(6585): 1116-1121, 2022 03 11.
Artigo em Inglês | MEDLINE | ID: mdl-35271324

RESUMO

We have come a long way since the start of the COVID-19 pandemic-from hoarding toilet paper and wiping down groceries to sending our children back to school and vaccinating billions. Over this period, the global community of epidemiologists and evolutionary biologists has also come a long way in understanding the complex and changing dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19. In this Review, we retrace our steps through the questions that this community faced as the pandemic unfolded. We focus on the key roles that mathematical modeling and quantitative analyses of empirical data have played in allowing us to address these questions and ultimately to better understand and control the pandemic.


Assuntos
Vacinas contra COVID-19 , COVID-19/epidemiologia , Controle de Doenças Transmissíveis , Pandemias , SARS-CoV-2 , Número Básico de Reprodução , COVID-19/prevenção & controle , COVID-19/transmissão , COVID-19/virologia , Modelos Epidemiológicos , Humanos , Modelos Teóricos , Quarentena , SARS-CoV-2/genética , SARS-CoV-2/patogenicidade
11.
Virus Evol ; 8(1): veac011, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35317348

RESUMO

In early 2020, as diagnostic and surveillance responses for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ramped up, attention focused primarily on returning international travelers. Here, we build on existing studies characterizing early patterns of SARS-CoV-2 spread within the USA by analyzing detailed clinical, molecular, and viral genomic data from the state of Georgia through March 2020. We find evidence for multiple early introductions into Georgia, despite relatively sparse sampling. Most sampled sequences likely stemmed from a single or small number of introductions from Asia three weeks prior to the state's first detected infection. Our analysis of sequences from domestic travelers demonstrates widespread circulation of closely related viruses in multiple US states by the end of March 2020. Our findings indicate that the exclusive focus on identifying SARS-CoV-2 in returning international travelers early in the pandemic may have led to a failure to recognize locally circulating infections for several weeks and point toward a critical need for implementing rapid, broadly targeted surveillance efforts for future pandemics.

12.
Pharmacogenet Genomics ; 21(6): 333-40, 2011 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-21562465

RESUMO

BACKGROUND/AIMS: Liver X receptor-α (LXRA) is a nuclear receptor that regulates genes important in cholesterol homeostasis and inflammation. Several single nucleotide polymorphisms (SNPs) in the LXRA gene (NR1H3) have been earlier associated with metabolic phenotypes (dyslipidemia and elevated body mass index). Metabolic dysregulation is a major contributor to coronary disease; therefore, we assessed LXRA in International Verapamil Sustained Release SR Trandolapril Study Genetic Substudy (INVEST-GENES), a genetic-substudy of a large clinical trial in patients with hypertension and coronary artery disease. METHODS: Seven tag SNPs in the LXRA gene region (NR1H3) were selected for study: rs11039149, rs12221497, rs2279238, rs7120118, rs326213, rs11039159, and rs10501321. One thousand fifty-nine patients were genotyped from the INVEST-GENES case-control set (verapamil-sustained release-based or atenolol-based treatment strategies) that comprised of 297 cases frequency matched (approximately 2.5:1) with that of event-free controls by sex and race. The primary outcome was defined as first occurrence of all-cause death, nonfatal myocardial infarction, or nonfatal stroke. Adjusted odds ratios (ORs) were calculated using logistic regression. RESULTS: Three of the seven SNPs were associated with significant effects on the primary outcome in nonBlacks. The variant G allele of rs11039149 and the variant A allele of rs12221497 were associated with reduced risk of experiencing the primary outcome [OR: 0.62, confidence interval (CI): 0.45-0.85, P=0.003 and OR: 0.60, CI: 0.39-0.91, P=0.016, respectively]. The rs2279238 genotype was associated with a significant increase in risk for the primary outcome (OR: 1.42, CI: 1.03-1.95, P=0.03). Furthermore, there was a significant genotype-treatment strategy interaction for carriers of the variant T allele of rs2279238 (OR for verapamil-sustained release strategy compared with atenolol strategy: 2.86, CI: 1.50-5.46, P=0.0015). Diplotype analyses showed that the SNPs are rarely coinherited and support the directionally opposite effects of the SNPs on the primary outcome. CONCLUSION: LXRA genotypes were associated with variable risk for cardiovascular outcomes and pharmacogenetic effect in INVEST-GENES. These novel findings suggest that LXRA is a genetic/pharmacogenetic target that should be further explored.


Assuntos
Anti-Hipertensivos/uso terapêutico , Doença da Artéria Coronariana/complicações , Hipertensão/tratamento farmacológico , Hipertensão/etiologia , Receptores Nucleares Órfãos/genética , Polimorfismo de Nucleotídeo Único/genética , Idoso , Atenolol/uso terapêutico , Índice de Massa Corporal , Bloqueadores dos Canais de Cálcio/uso terapêutico , Estudos de Casos e Controles , DNA/genética , Feminino , Genótipo , Humanos , Receptores X do Fígado , Masculino , Reação em Cadeia da Polimerase , Estudos Prospectivos , Resultado do Tratamento , Verapamil/uso terapêutico
13.
Sci Transl Med ; 13(617): eabh1803, 2021 Oct 27.
Artigo em Inglês | MEDLINE | ID: mdl-34705523

RESUMO

A reanalysis of SARS-CoV-2 deep sequencing data from donor-recipient pairs indicates that transmission bottlenecks are very narrow (one to three virions).


Assuntos
COVID-19 , SARS-CoV-2 , Áustria , Genômica , Humanos , Mutação/genética
14.
Nat Commun ; 11(1): 5518, 2020 11 02.
Artigo em Inglês | MEDLINE | ID: mdl-33139704

RESUMO

Full genome sequences are increasingly used to track the geographic spread and transmission dynamics of viral pathogens. Here, with a focus on Israel, we sequence 212 SARS-CoV-2 sequences and use them to perform a comprehensive analysis to trace the origins and spread of the virus. We find that travelers returning from the United States of America significantly contributed to viral spread in Israel, more than their proportion in incoming infected travelers. Using phylodynamic analysis, we estimate that the basic reproduction number of the virus was initially around 2.5, dropping by more than two-thirds following the implementation of social distancing measures. We further report high levels of transmission heterogeneity in SARS-CoV-2 spread, with between 2-10% of infected individuals resulting in 80% of secondary infections. Overall, our findings demonstrate the effectiveness of social distancing measures for reducing viral spread.


Assuntos
Betacoronavirus/genética , Doenças Transmissíveis Importadas/virologia , Infecções por Coronavirus/transmissão , Genoma Viral/genética , Pneumonia Viral/transmissão , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Sequência de Bases , Número Básico de Reprodução/estatística & dados numéricos , COVID-19 , Criança , Pré-Escolar , Doenças Transmissíveis Importadas/epidemiologia , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/prevenção & controle , Feminino , Humanos , Lactente , Recém-Nascido , Israel/epidemiologia , Masculino , Pessoa de Meia-Idade , Pandemias/prevenção & controle , Filogenia , Pneumonia Viral/epidemiologia , Pneumonia Viral/prevenção & controle , Distância Psicológica , RNA Viral/genética , SARS-CoV-2 , Análise de Sequência de RNA , Estados Unidos , Adulto Jovem
15.
medRxiv ; 2020 Jul 10.
Artigo em Inglês | MEDLINE | ID: mdl-32676620

RESUMO

Evidence-based public health approaches that minimize the introduction and spread of new SARS-CoV-2 transmission clusters are urgently needed in the United States and other countries struggling with expanding epidemics. Here we analyze 247 full-genome SARS-CoV-2 sequences from two nearby communities in Wisconsin, USA, and find surprisingly distinct patterns of viral spread. Dane County had the 12th known introduction of SARS-CoV-2 in the United States, but this did not lead to descendant community spread. Instead, the Dane County outbreak was seeded by multiple later introductions, followed by limited community spread. In contrast, relatively few introductions in Milwaukee County led to extensive community spread. We present evidence for reduced viral spread in both counties, and limited viral transmission between counties, following the statewide Safer-at-Home public health order, which went into effect 25 March 2020. Our results suggest that early containment efforts suppressed the spread of SARS-CoV-2 within Wisconsin.

16.
Nat Commun ; 11(1): 5558, 2020 11 03.
Artigo em Inglês | MEDLINE | ID: mdl-33144575

RESUMO

Evidence-based public health approaches that minimize the introduction and spread of new SARS-CoV-2 transmission clusters are urgently needed in the United States and other countries struggling with expanding epidemics. Here we analyze 247 full-genome SARS-CoV-2 sequences from two nearby communities in Wisconsin, USA, and find surprisingly distinct patterns of viral spread. Dane County had the 12th known introduction of SARS-CoV-2 in the United States, but this did not lead to descendant community spread. Instead, the Dane County outbreak was seeded by multiple later introductions, followed by limited community spread. In contrast, relatively few introductions in Milwaukee County led to extensive community spread. We present evidence for reduced viral spread in both counties following the statewide "Safer at Home" order, which went into effect 25 March 2020. Our results suggest patterns of SARS-CoV-2 transmission may vary substantially even in nearby communities. Understanding these local patterns will enable better targeting of public health interventions.


Assuntos
Betacoronavirus/genética , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/transmissão , Genoma Viral/genética , Pneumonia Viral/epidemiologia , Pneumonia Viral/transmissão , COVID-19 , Infecções por Coronavirus/prevenção & controle , Geografia , Humanos , Programas de Rastreamento/métodos , Epidemiologia Molecular/métodos , Pandemias/prevenção & controle , Pneumonia Viral/prevenção & controle , Distância Psicológica , Dispositivos de Proteção Respiratória , SARS-CoV-2 , Estados Unidos/epidemiologia , Wisconsin/epidemiologia
17.
J Orthop Sports Phys Ther ; 49(1): 5-16, 2019 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-30208795

RESUMO

BACKGROUND: Knowledge of patellofemoral osteoarthritis (OA) pain trajectories is vital to helping clinicians and patients make shared disease-specific decisions regarding treatment options and coping strategies. OBJECTIVES: To describe the pain trajectories of people living with patellofemoral OA who present to a chronic care management program, and to explore baseline characteristics associated with different trajectories. METHODS: In this prospective longitudinal cohort study, 88 participants who presented to a chronic care management program reported their worst pain over the previous week at baseline and at 6, 12, 18, and 26 weeks using a 10-cm visual analog scale. Trajectories (classes) were identified using latent class growth analysis. Demographics, pain, physical performance, strength, quality of life, mental health, and lower limb/foot structural measures obtained at baseline were assessed for association with trajectory class membership. RESULTS: Individuals in class 1 (28%) exhibited high, persistent pain from baseline (7.8 ± 1.7 cm), which continued over time (P = .52). Class 2 (57%) displayed moderate baseline pain (4.8 ± 1.8 cm), which also remained persistent (P = .97). Individuals in class 3 (15%) showed low, improving pain (baseline pain, 2.6 ± 1.2 cm) over time (P = .017). At baseline, poor Knee injury and Osteoarthritis Outcome Score (KOOS) scores, local and proximal sensitivity to pressure, and lower knee extensor strength were associated with increased odds of following the high-pain trajectory (range [95% confidence interval], 1.03 [1.00, 1.07] to 16.24 [2.53, 104.34]). CONCLUSION: Distinct pain trajectories appear to exist in people with patellofemoral OA presenting to a chronic care management program. Baseline variables may be useful for identifying individuals at risk of poorer prognosis. Larger studies are needed to confirm the efficacy of this finding. LEVEL OF EVIDENCE: Prognosis, level 2b. J Orthop Sports Phys Ther 2019;49(1):5-16. Epub 12 Sep 2018. doi:10.2519/jospt.2019.8354.


Assuntos
Osteoartrite do Joelho/complicações , Dor/diagnóstico , Dor/etiologia , Idoso , Terapia por Exercício , Feminino , Humanos , Estudos Longitudinais , Masculino , Pessoa de Meia-Idade , Força Muscular/fisiologia , Osteoartrite do Joelho/fisiopatologia , Osteoartrite do Joelho/reabilitação , Medição da Dor , Medidas de Resultados Relatados pelo Paciente , Estudos Prospectivos , Autocuidado , Redução de Peso
18.
Am J Epidemiol ; 167(12): 1511-7, 2008 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-18417495

RESUMO

The authors propose a regression-based approach for obtaining multiday estimates of the adverse health effects of ambient particulate matter less than 10 microm in diameter (PM(10)) when daily PM(10) time-series data are unavailable. This situation is common in the United States, because most US cities take PM(10) measurements every 6 days. Current evidence suggests that adverse effects of PM(10) are not concentrated on a single day but rather are spread out over multiple days, so the unavailability of daily PM(10) data presents a problem for the estimation of these effects. The proposed model estimates weights that are used to construct a linear combination of single-lag PM(10) effect estimates obtained from the available PM(10) data. It is shown that this new approach provides estimates of the effect of PM(10) on mortality that have less bias and mean squared error than currently available methods. Application of this method to the US cities contained in the National Morbidity, Mortality, and Air Pollution Study database produces an estimated national average effect of PM(10) on nonaccidental mortality in persons over age 65 years, corresponding to a 0.32% increase per 10-microg/m(3) increment in PM(10). The estimated effects for cardiorespiratory mortality and other mortality are 0.34% and 0.22%, respectively.


Assuntos
Poluição do Ar/efeitos adversos , Material Particulado/efeitos adversos , Análise de Regressão , Estatística como Assunto , Coleta de Dados , Métodos Epidemiológicos , Humanos , Modelos Estatísticos , Estatística como Assunto/métodos , Fatores de Tempo , Estados Unidos
19.
Microb Genom ; 4(10)2018 10.
Artigo em Inglês | MEDLINE | ID: mdl-30303479

RESUMO

Whole genome sequencing in conjunction with traditional epidemiology has been used to reconstruct transmission networks of Mycobacterium tuberculosis during outbreaks. Given its low mutation rate, genetic diversity within M. tuberculosis outbreaks can be extremely limited - making it difficult to determine precisely who transmitted to whom. In addition to consensus SNPs (cSNPs), examining heterogeneous alleles (hSNPs) has been proposed to improve resolution. However, few studies have examined the potential biases in detecting these hSNPs. Here, we analysed genome sequence data from 25 specimens from British Columbia, Canada. Specimens were sequenced to a depth of 112-296×. We observed biases in read depth, base quality, strand distribution and read placement where possible hSNPs were initially identified, so we applied conservative filters to reduce false positives. Overall, there was phylogenetic concordance between the observed 2542 cSNP and 63 hSNP loci. Furthermore, we identified hSNPs shared exclusively by epidemiologically linked patients, supporting their use in transmission inferences. We conclude that hSNPs may add resolution to transmission networks, particularly where the overall genetic diversity is low.


Assuntos
Surtos de Doenças , Genoma Bacteriano , Taxa de Mutação , Mycobacterium tuberculosis/genética , Filogenia , Polimorfismo de Nucleotídeo Único , Tuberculose Pulmonar , Sequenciamento Completo do Genoma , Colúmbia Britânica/epidemiologia , Humanos , Mycobacterium tuberculosis/isolamento & purificação , Tuberculose Pulmonar/epidemiologia , Tuberculose Pulmonar/genética , Tuberculose Pulmonar/transmissão
20.
J Am Coll Surg ; 204(2): 193-200, 2007 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-17254922

RESUMO

BACKGROUND: Unplanned hospital readmissions after surgical treatment for breast cancer are an indicator of morbidity. We explore the relationship between the rate of unplanned hospital readmissions within 42 days of initial treatment and various factors, including tumor size and histology, lymph node involvement, type of surgical treatment, mastectomy, or breast-conserving surgery, and patient demographics. METHODS: Linked Western Australian cancer mortality and hospital morbidity data were used in the assessment of readmissions within a period of 42 days after initial surgical treatment for breast cancer. Planned admissions for adjuvant treatment such as chemotherapy or radiotherapy were deleted. Survival models for multiple events per subject were applied to analyze the data. RESULTS: The analysis reveals that patients more likely to experience lower recurrence of short-term unplanned hospital readmissions include those with smaller tumors, private insurance, and who reside in metropolitan areas. The model also includes important two-way interaction terms involving tumor histology, area of residence, and surgical treatment, and between lymph node involvement and patient age. CONCLUSIONS: This study suggests that the choice of breast-conserving surgery as a treatment for breast cancer does not invariably result in better postoperative morbidity, but rather, that other factors, including tumor size and patient demographics, play a critical role in the short term. These results differ from a previous study of longterm hospital readmissions-country of birth and method of payment were found to be associated with short-term hospital admission but not with longterm readmissions.


Assuntos
Neoplasias da Mama/cirurgia , Readmissão do Paciente/estatística & dados numéricos , Fatores Etários , Neoplasias da Mama/patologia , Carcinoma Ductal de Mama/patologia , Carcinoma Ductal de Mama/cirurgia , Carcinoma Lobular/patologia , Carcinoma Lobular/cirurgia , Etnicidade/estatística & dados numéricos , Feminino , Humanos , Seguro Saúde/estatística & dados numéricos , Linfonodos/patologia , Mastectomia/estatística & dados numéricos , Mastectomia Segmentar/estatística & dados numéricos , Estadiamento de Neoplasias , Características de Residência/estatística & dados numéricos , Fatores de Risco , Taxa de Sobrevida , Saúde da População Urbana/estatística & dados numéricos , Austrália Ocidental
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