Last data update: May 13, 2024. (Total: 46773 publications since 2009)
Records 1-10 (of 10 Records) |
Query Trace: Watanabe E[original query] |
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Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution (preprint)
Huddleston J , Barnes JR , Rowe T , Xu X , Kondor R , Wentworth DE , Whittaker L , Ermetal B , Daniels RS , McCauley JW , Fujisaki S , Nakamura K , Kishida N , Watanabe S , Hasegawa H , Barr I , Subbarao K , Neher RA , Bedford T . bioRxiv 2020 2020.06.12.145151 Seasonal influenza virus A/H3N2 is a major cause of death globally. Vaccination remains the most effective preventative. Rapid mutation of hemagglutinin allows viruses to escape adaptive immunity. This antigenic drift necessitates regular vaccine updates. Effective vaccine strains need to represent H3N2 populations circulating one year after strain selection. Experts select strains based on experimental measurements of antigenic drift and predictions made by models from hemagglutinin sequences. We developed a novel influenza forecasting framework that integrates phenotypic measures of antigenic drift and functional constraint with previously published sequence-only fitness estimates. Forecasts informed by phenotypic measures of antigenic drift consistently outperformed previous sequence-only estimates, while sequence-only estimates of functional constraint surpassed more comprehensive experimentally-informed estimates. Importantly, the best models integrated estimates of both functional constraint and either antigenic drift phenotypes or recent population growth.Competing Interest StatementThe authors have declared no competing interest. |
Using Tribal Data Linkages to Improve the Quality of American Indian Cancer Data in Michigan
Weber TL , Copeland G , Pingatore N , Schmid KK , Jim MA , Watanabe-Galloway S . J Health Care Poor Underserved 2019 30 (3) 1237-1247 This study examines the extent to which data linkages between Indian Health Service, tribal data, and cancer registries affect cancer incidence rates among American Indians/Alaska Natives (AI/ANs) in Michigan. The incidence of tobacco- and alcohol-associated cancers for 1995-2012 was analyzed to compare rates of the Upper Peninsula (UP) and Lower Peninsula (LP) in Michigan and among AI/ANs and non-Hispanic Whites (NHWs). Complete linkage resulted in 1,352 additional AI/AN cases; 141 cases were linked via IHS records alone, while 373 were linked via tribal records alone; 838 were linked through both IHS and tribal records. Age-adjusted incidence rates for AI/ANs increased from 214.39 per 100,000 to 405.41 per 100,000, similar to that of NHWs after complete linkage (421.46 per 100,000). In the UP, AI/ANs had age-adjusted incidence rates 1.67 times higher than NHWs (596.69 per 100,000 vs. 356.32 per 100,000 respectively). This study indicates a substantial number of AI/AN cancer cases remain misclassified in Michigan. |
An external quality assessment feasibility study; cross laboratory comparison of haemagglutination inhibition assay and microneutralization assay performance for seasonal influenza serology testing: A FLUCOP study
Waldock J , Weiss CD , Wang W , Levine MZ , Jefferson SN , Ho S , Hoschler K , Londt BZ , Masat E , Carolan L , Sánchez-Ovando S , Fox A , Watanabe S , Akimoto M , Sato A , Kishida N , Buys A , Maake L , Fourie C , Caillet C , Raynaud S , Webby RJ , DeBeauchamp J , Cox RJ , Lartey SL , Trombetta CM , Marchi S , Montomoli E , Sanz-Muñoz I , Eiros JM , Sánchez-Martínez J , Duijsings D , Engelhardt OG . Front Immunol 2023 14 1129765 INTRODUCTION: External Quality Assessment (EQA) schemes are designed to provide a snapshot of laboratory proficiency, identifying issues and providing feedback to improve laboratory performance and inter-laboratory agreement in testing. Currently there are no international EQA schemes for seasonal influenza serology testing. Here we present a feasibility study for conducting an EQA scheme for influenza serology methods. METHODS: We invited participant laboratories from industry, contract research organizations (CROs), academia and public health institutions who regularly conduct hemagglutination inhibition (HAI) and microneutralization (MN) assays and have an interest in serology standardization. In total 16 laboratories returned data including 19 data sets for HAI assays and 9 data sets for MN assays. RESULTS: Within run analysis demonstrated good laboratory performance for HAI, with intrinsically higher levels of intra-assay variation for MN assays. Between run analysis showed laboratory and strain specific issues, particularly with B strains for HAI, whilst MN testing was consistently good across labs and strains. Inter-laboratory variability was higher for MN assays than HAI, however both assays showed a significant reduction in inter-laboratory variation when a human sera pool is used as a standard for normalization. DISCUSSION: This study has received positive feedback from participants, highlighting the benefit such an EQA scheme would have on improving laboratory performance, reducing inter laboratory variation and raising awareness of both harmonized protocol use and the benefit of biological standards for seasonal influenza serology testing. |
Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution.
Huddleston J , Barnes JR , Rowe T , Xu X , Kondor R , Wentworth DE , Whittaker L , Ermetal B , Daniels RS , McCauley JW , Fujisaki S , Nakamura K , Kishida N , Watanabe S , Hasegawa H , Barr I , Subbarao K , Barrat-Charlaix P , Neher RA , Bedford T . Elife 2020 9 Seasonal influenza virus A/H3N2 is a major cause of death globally. Vaccination remains the most effective preventative. Rapid mutation of hemagglutinin allows viruses to escape adaptive immunity. This antigenic drift necessitates regular vaccine updates. Effective vaccine strains need to represent H3N2 populations circulating one year after strain selection. Experts select strains based on experimental measurements of antigenic drift and predictions made by models from hemagglutinin sequences. We developed a novel influenza forecasting framework that integrates phenotypic measures of antigenic drift and functional constraint with previously published sequence-only fitness estimates. Forecasts informed by phenotypic measures of antigenic drift consistently outperformed previous sequence- only estimates, while sequence-only estimates of functional constraint surpassed more comprehensive experimentally-informed estimates. Importantly, the best models integrated estimates of both functional constraint and either antigenic drift phenotypes or recent population growth. |
CDC's multiple approaches to safeguard the health, safety, and resilience of Ebola responders
Klomp RW , Jones L , Watanabe E , Thompson WW . Prehosp Disaster Med 2019 35 (1) 1-7 Over 27,000 people were sickened by Ebola and over 11,000 people died between March of 2014 and June of 2016. The US Centers for Disease Control and Prevention (CDC; Atlanta, Georgia USA) was one of many public health organizations that sought to stop this outbreak. This agency deployed almost 2,000 individuals to West Africa during that timeframe. Deployment to these countries exposed these individuals to a wide variety of dangers, stressors, and risks.Being concerned about the at-risk populations in Africa, and also the well-being of its professionals who willingly deployed, the CDC did several things to help safeguard the health, safety, and resilience of these team members before, during, and after deployment.The accompanying special report highlights innovative pre-deployment training initiatives, customized screening processes, and post-deployment outreach efforts intended to protect and support the public health professionals fighting Ebola. Before deploying, the CDC team members were expected to participate in both internally-created and externally-provided trainings. These ranged from pre-deployment briefings, to Preparing for Work Overseas (PFWO) and Public Health Readiness Certificate Program (PHRCP) courses, to Incident Command System (ICS) 100, 200, and 400 courses.A small subset of non-clinical deployers also participated in a three-day training designed in collaboration with the Center for the Study of Traumatic Stress (CSTS; Bethesda, Maryland USA) to train individuals to assess and address the well-being and resilience of themselves and their teammates in the field during a deployment. Participants in this unique training were immersed in a Virtual Reality Environment (VRE) that simulated deployment to one of seven different types of emergencies.The CDC leadership also requested a pre-deployment screening process that helped professionals in the CDC's Occupational Health Clinic (OHC) determine whether or not individuals were at an increased risk of negative outcomes by participating in a rigorous deployment at that time.When deployers returned from the field, they received personalized invitations to participate in a voluntary, confidential, post-deployment operational debriefing one-on-one or in a group.Implementing these approaches provided more information to clinical decision makers about the readiness of deployers. It provided deployers with a greater awareness of the kinds of challenges they were likely to face in the field. The post-deployment outreach efforts reminded staff that their contributions were appreciated and there were resources available if they needed help processing any of the potentially-traumatizing things they may have experienced. |
Selection of antigenically advanced variants of seasonal influenza viruses
Li C , Hatta M , Burke DF , Ping J , Zhang Y , Ozawa M , Taft AS , Das SC , Hanson AP , Song J , Imai M , Wilker PR , Watanabe T , Watanabe S , Ito M , Iwatsuki-Horimoto K , Russell CA , James SL , Skepner E , Maher EA , Neumann G , Klimov AI , Kelso A , McCauley J , Wang D , Shu Y , Odagiri T , Tashiro M , Xu X , Wentworth DE , Katz JM , Cox NJ , Smith DJ , Kawaoka Y . Nat Microbiol 2016 1 (6) 16058 Influenza viruses mutate frequently, necessitating constant updates of vaccine viruses. To establish experimental approaches that may complement the current vaccine strain selection process, we selected antigenic variants from human H1N1 and H3N2 influenza virus libraries possessing random mutations in the globular head of the haemagglutinin protein (which includes the antigenic sites) by incubating them with human and/or ferret convalescent sera to human H1N1 and H3N2 viruses. We also selected antigenic escape variants from human viruses treated with convalescent sera and from mice that had been previously immunized against human influenza viruses. Our pilot studies with past influenza viruses identified escape mutants that were antigenically similar to variants that emerged in nature, establishing the feasibility of our approach. Our studies with contemporary human influenza viruses identified escape mutants before they caused an epidemic in 2014-2015. This approach may aid in the prediction of potential antigenic escape variants and the selection of future vaccine candidates before they become widespread in nature. |
Enteric bacteria promote human and mouse norovirus infection of B cells
Jones MK , Watanabe M , Zhu S , Graves CL , Keyes LR , Grau KR , Gonzalez-Hernandez MB , Iovine NM , Wobus CE , Vinje J , Tibbetts SA , Wallet SM , Karst SM . Science 2014 346 (6210) 755-9 The cell tropism of human noroviruses and the development of an in vitro infection model remain elusive. Although susceptibility to individual human norovirus strains correlates with an individual's histo-blood group antigen (HBGA) profile, the biological basis of this restriction is unknown. We demonstrate that human and mouse noroviruses infected B cells in vitro and likely in vivo. Human norovirus infection of B cells required the presence of HBGA-expressing enteric bacteria. Furthermore, mouse norovirus replication was reduced in vivo when the intestinal microbiota was depleted by means of oral antibiotic administration. Thus, we have identified B cells as a cellular target of noroviruses and enteric bacteria as a stimulatory factor for norovirus infection, leading to the development of an in vitro infection model for human noroviruses. |
Tumor necrosis factor -308 polymorphism (rs1800629) is associated with mortality and ventilator duration in 1057 Caucasian patients.
Watanabe E , Zehnbauer BA , Oda S , Sato Y , Hirasawa H , Buchman TG . Cytokine 2012 60 (1) 249-56 PURPOSE: Management of sepsis in critically ill patients remains difficult and requires prolonged intensive care. Genetic testing has been proposed as a strategy to identify patients at risk for adverse outcome of critical illnesses. Therefore, we wished to determine the influence of heredity on predisposition to poor outcome and on duration of ventilator support of intensive care unit (ICU) patients. METHODS: A study was conducted from July 2001 to December 2005 in heterogeneous population of patients from 12 US ICUs represented by the Genetic Predisposition to Severe Sepsis (GenPSS) archive. In 1057 Caucasian critically ill patients with SAPS II probability of survival of >0.2 in the US, six functional single nucleotide polymorphisms in relation to inflammatory cytokines and innate immunity (rs1800629, rs16944, rs1800795, rs1800871, rs2569190, and rs909253) were evaluated in terms of mortality and ventilator free days. RESULTS: The AA homozygote of TNF(-308) (rs1800629) was most over-represented in the deceased patient group (P=0.015 with recessive model). The carriage of the TNF(-308)*AA genotype showed significantly higher odds ratio of 2.67(1.29-5.55) (P=0.008) after adjustment with the covariates. However, the presence of 1, 2, or 3 acute organ dysfunctions was larger prognostic factors for the adverse outcome (OR(95%CI)=2.98(2.00-4.45), 4.01(2.07-7.77), or 19.95(4.99-79.72), P<0.001 for all). Kaplan-Mayer plot on ventilator duration of TNF(-308)*AA patient significantly diverged from that of TNF(-308)*(GG+GA) ((AA v GG+GA), Adjusted HR(95%CI)=2.53(1.11-5.79) with Cox regression, P=0.028). CONCLUSIONS: TNF(-308)*AA is significantly associated with susceptibility to adverse outcome and to longer ventilator duration. Therefore, heredity likely affects both predisposition to ICU prognosis as well as the resource utilization. |
No interactions between previously associated 2-hour glucose gene variants and physical activity or BMI on 2-hour glucose levels.
Scott RA , Chu AY , Grarup N , Manning AK , Hivert MF , Shungin D , Tonjes A , Yesupriya A , Barnes D , Bouatia-Naji N , Glazer NL , Jackson AU , Kutalik Z , Lagou V , Marek D , Rasmussen-Torvik LJ , Stringham HM , Tanaka T , Aadahl M , Arking DE , Bergmann S , Boerwinkle E , Bonnycastle LL , Bornstein SR , Brunner E , Bumpstead SJ , Brage S , Carlson OD , Chen H , Chen YD , Chines PS , Collins FS , Couper DJ , Dennison EM , Dowling NF , Egan JS , Ekelund U , Erdos MR , Forouhi NG , Fox CS , Goodarzi MO , Grässler J , Gustafsson S , Hallmans G , Hansen T , Hingorani A , Holloway JW , Hu FB , Isomaa B , Jameson KA , Johansson I , Jonsson A , Jørgensen T , Kivimaki M , Kovacs P , Kumari M , Kuusisto J , Laakso M , Lecoeur C , Lévy-Marchal C , Li G , Loos RJ , Lyssenko V , Marmot M , Marques-Vidal P , Morken MA , Müller G , North KE , Pankow JS , Payne F , Prokopenko I , Psaty BM , Renström F , Rice K , Rotter JI , Rybin D , Sandholt CH , Sayer AA , Shrader P , Schwarz PE , Siscovick DS , Stancáková A , Stumvoll M , Teslovich TM , Waeber G , Williams GH , Witte DR , Wood AR , Xie W , Boehnke M , Cooper C , Ferrucci L , Froguel P , Groop L , Kao WH , Vollenweider P , Walker M , Watanabe RM , Pedersen O , Meigs JB , Ingelsson E , Barroso I , Florez JC , Franks PW , Dupuis J , Wareham NJ , Langenberg C . Diabetes 2012 61 (5) 1291-6 Gene-lifestyle interactions have been suggested to contribute to the development of type 2 diabetes. Glucose levels 2 h after a standard 75-g glucose challenge are used to diagnose diabetes and are associated with both genetic and lifestyle factors. However, whether these factors interact to determine 2-h glucose levels is unknown. We meta-analyzed single nucleotide polymorphism (SNP) x BMI and SNP x physical activity (PA) interaction regression models for five SNPs previously associated with 2-h glucose levels from up to 22 studies comprising 54,884 individuals without diabetes. PA levels were dichotomized, with individuals below the first quintile classified as inactive (20%) and the remainder as active (80%). BMI was considered a continuous trait. Inactive individuals had higher 2-h glucose levels than active individuals (beta = 0.22 mmol/L [95% CI 0.13-0.31], P = 1.63 x 10(-6)). All SNPs were associated with 2-h glucose (beta = 0.06-0.12 mmol/allele, P ≤ 1.53 x 10(-7)), but no significant interactions were found with PA (P > 0.18) or BMI (P ≥ 0.04). In this large study of gene-lifestyle interaction, we observed no interactions between genetic and lifestyle factors, both of which were associated with 2-h glucose. It is perhaps unlikely that top loci from genome-wide association studies will exhibit strong subgroup-specific effects, and may not, therefore, make the best candidates for the study of interactions. |
Outbreak of Neisseria meningitidis C in workers at a large food-processing plant in Brazil: challenges of controlling disease spread to the larger community
Iser BP , Lima HC , De Moraes C , De Almeida RP , Watanabe LT , Alves SL , Lemos AP , Gorla MC , Goncalves MG , Dos Santos DA , Sobel J . Epidemiol Infect 2012 140 (5) 906-15 SUMMARY: An outbreak of meningococcal disease (MD) with severe morbidity and mortality was investigated in midwestern Brazil in order to identify control measures. A MD case was defined as isolation of Neisseria meningitidis, or detection of polysaccharide antigen in a sterile site, or presence of clinical purpura fulminans, or an epidemiological link with a laboratory-confirmed case-patient, between June and August 2008. In 8 out of 16 MD cases studied, serogroup C ST103 complex was identified. Five (31%) cases had neurological findings and five (31%) died. The attack rate was 12 cases/100,000 town residents and 60 cases/100,000 employees in a large local food-processing plant. We conducted a matched case-control study of eight primary laboratory-confirmed cases (1:4). Factors associated with illness in single variable analysis were work at the processing plant [matched odds ratio (mOR) 22, 95% confidence interval (CI) 2.3-207.7, P<0.01], and residing <1 year in Rio Verde (mOR 7, 95% CI 1.11-43.9, P<0.02). Mass vaccination (>10 000 plant employees) stopped propagation in the plant, but not in the larger community. |
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