Last data update: May 13, 2024. (Total: 46773 publications since 2009)
Records 1-8 (of 8 Records) |
Query Trace: Smithee S[original query] |
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Epidemiology of SARS-CoV-2 transmission and superspreading in Salt Lake County, Utah, March-May 2020
Walker J , Tran T , Lappe B , Gastanaduy P , Paul P , Kracalik IT , Fields VL , Lopez A , Schwartz A , Lewis NM , Tate JE , Kirking HL , Hall AJ , Pevzner E , Khong H , Smithee M , Lowry J , Dunn A , Kiphibane T , Tran CH . PLoS One 2023 18 (6) e0275125 BACKGROUND: Understanding the drivers of SARS-CoV-2 transmission can inform the development of interventions. We evaluated transmission identified by contact tracing investigations between March-May 2020 in Salt Lake County, Utah, to quantify the impact of this intervention and identify risk factors for transmission. METHODS: RT-PCR positive and untested symptomatic contacts were classified as confirmed and probable secondary case-patients, respectively. We compared the number of case-patients and close contacts generated by different groups, and used logistic regression to evaluate factors associated with transmission. RESULTS: Data were collected on 184 index case-patients and up to six generations of contacts. Of 1,499 close contacts, 374 (25%) were classified as secondary case-patients. Decreased transmission odds were observed for contacts aged <18 years (OR = 0.55 [95% CI: 0.38-0.79]), versus 18-44 years, and for workplace (OR = 0.36 [95% CI: 0.23-0.55]) and social (OR = 0.44 [95% CI: 0.28-0.66]) contacts, versus household contacts. Higher transmission odds were observed for case-patient's spouses than other household contacts (OR = 2.25 [95% CI: 1.52-3.35]). Compared to index case-patients identified in the community, secondary case-patients identified through contract-tracing generated significantly fewer close contacts and secondary case-patients of their own. Transmission was heterogeneous, with 41% of index case-patients generating 81% of directly-linked secondary case-patients. CONCLUSIONS: Given sufficient resources and complementary public health measures, contact tracing can contain known chains of SARS-CoV-2 transmission. Transmission is associated with age and exposure setting, and can be highly variable, with a few infections generating a disproportionately high share of onward transmission. |
Coronavirus Disease Contact Tracing Outcomes and Cost, Salt Lake County, Utah, USA, March-May 2020.
Fields VL , Kracalik IT , Carthel C , Lopez A , Schwartz A , Lewis NM , Bray M , Claflin C , Jorgensen K , Khong H , Richards W , Risk I , Smithee M , Clawson M , Booth LC , Scribellito T , Lowry J , Huynh J , Davis L , Birch H , Tran T , Walker J , Fry A , Hall A , Baker J , Pevzner E , Dunn AC , Tate JE , Kirking HL , Kiphibane T , Tran CH . Emerg Infect Dis 2021 27 (12) 2999-3008 Outcomes and costs of coronavirus disease (COVID-19) contact tracing are limited. During March-May 2020, we constructed transmission chains from 184 index cases and 1,499 contacts in Salt Lake County, Utah, USA, to assess outcomes and estimate staff time and salaries. We estimated 1,102 staff hours and $29,234 spent investigating index cases and contacts. Among contacts, 374 (25%) had COVID-19; secondary case detection rate was ≈31% among first-generation contacts, ≈16% among second- and third-generation contacts, and ≈12% among fourth-, fifth-, and sixth-generation contacts. At initial interview, 51% (187/370) of contacts were COVID-19-positive; 35% (98/277) became positive during 14-day quarantine. Median time from symptom onset to investigation was 7 days for index cases and 4 days for first-generation contacts. Contact tracing reduced the number of cases between contact generations and time between symptom onset and investigation but required substantial resources. Our findings can help jurisdictions allocate resources for contact tracing. |
Development of a new oral poliovirus vaccine for the eradication end game using codon deoptimization.
Konopka-Anstadt Jennifer L, Campagnoli Ray, Vincent Annelet, Shaw Jing, Wei Ling, Wynn Nhien T, Smithee Shane E, Bujaki Erika, Te Yeh Ming, Laassri Majid, Zagorodnyaya Tatiana, Weiner Amy J, Chumakov Konstantin, Andino Raul, Macadam Andrew, Kew Olen, Burns Cara C. NPJ vaccines 2020 Mar 5(1) 26 . NPJ vaccines 2020 Mar 5(1) 26 Konopka-Anstadt Jennifer L, Campagnoli Ray, Vincent Annelet, Shaw Jing, Wei Ling, Wynn Nhien T, Smithee Shane E, Bujaki Erika, Te Yeh Ming, Laassri Majid, Zagorodnyaya Tatiana, Weiner Amy J, Chumakov Konstantin, Andino Raul, Macadam Andrew, Kew Olen, Burns Cara C. NPJ vaccines 2020 Mar 5(1) 26 |
Pneumonia hospitalization coding changes associated with transition from the 9th to 10th Revision of International Classification of Diseases
Smithee RB , Markus TM , Soda E , Grijalva CG , Xing W , Shang N , Griffin MR , Lessa FC . Health Serv Res Manag Epidemiol 2020 7 2333392820939801 OBJECTIVES: To evaluate the impact of International Classification of Disease, 10th revision, Clinical Modification (ICD-10-CM) implementation on pneumonia hospitalizations rates, which had declined following pneumococcal conjugate vaccine introduction for infants in 2000. METHODS: We randomly selected records from a single hospital 1 year before (n = 500) and after (n = 500) October 2015 implementation of ICD-10-CM coding. We used a validated ICD-9-CM algorithm and translation of that algorithm to ICD-10-CM to identify pneumonia hospitalizations pre- and post-implementation, respectively. We recoded ICD-10-CM records to ICD-9-CM and vice versa. We calculated sensitivity and positive predictive value (PPV) of the ICD-10-CM algorithm using ICD-9-CM coding as the reference. We used sensitivity and PPV values to calculate an adjustment factor to apply to ICD-10 era rates to enable comparison with ICD-9-CM rates. We reviewed primary diagnoses of charts not meeting the pneumonia definition when recoded. RESULTS: Sensitivity and PPV of the ICD-10-CM algorithm were 94% and 92%, respectively, for young children and 74% and 79% for older adults. The estimated adjustment factor for ICD-10-CM period rates was -2.09% (95% credible region [CR], -7.71% to +3.0%) for children and +6.76% (95% CR, -3.06% to +16.7%) for older adults. We identified a change in coding adult charts that met the ICD-9-CM pneumonia definition that led to recoding in ICD-10-CM as chronic obstructive pulmonary disease (COPD) exacerbation. CONCLUSIONS: The ICD-10-CM algorithm derived from a validated ICD-9-CM algorithm should not introduce substantial bias for evaluating pneumonia trends in children. However, changes in coding of pneumonia associated with COPD in adults warrant further study. |
Development of a new oral poliovirus vaccine for the eradication end game using codon deoptimization.
Konopka-Anstadt JL , Campagnoli R , Vincent A , Shaw J , Wei L , Wynn NT , Smithee SE , Bujaki E , Te Yeh M , Laassri M , Zagorodnyaya T , Weiner AJ , Chumakov K , Andino R , Macadam A , Kew O , Burns CC . NPJ Vaccines 2020 5 (1) 26 Enormous progress has been made in global efforts to eradicate poliovirus, using live-attenuated Sabin oral poliovirus vaccine (OPV). However, as the incidence of disease due to wild poliovirus has declined, vaccine-derived poliovirus (VDPV) has emerged in areas of low-vaccine coverage. Coordinated global cessation of routine, type 2 Sabin OPV (OPV2) use has not resulted in fewer VDPV outbreaks, and continued OPV use in outbreak-response campaigns has seeded new emergences in low-coverage areas. The limitations of existing vaccines and current eradication challenges warranted development of more genetically stable OPV strains, most urgently for OPV2. Here, we report using codon deoptimization to further attenuate Sabin OPV2 by changing preferred codons across the capsid to non-preferred, synonymous codons. Additional modifications to the 5' untranslated region stabilized known virulence determinants. Testing of this codon-deoptimized new OPV2 candidate (nOPV2-CD) in cell and animal models demonstrated that nOPV2-CD is highly attenuated, grows sufficiently for vaccine manufacture, is antigenically indistinguishable from Sabin OPV2, induces neutralizing antibodies as effectively as Sabin OPV2, and unlike Sabin OPV2 is genetically stable and maintains an attenuation phenotype. In-human clinical trials of nOPV2-CD are ongoing, with potential for nOPV strains to serve as critical vaccine tools for achieving and maintaining polio eradication. |
Domain I of the 5' non-translated genomic region in coxsackievirus B3 RNA is not required for productive replication.
Jaramillo L , Smithee S , Tracy S , Chapman NM . Virology 2016 496 127-130 Domain I is a cloverleaf-like secondary structure at the 5' termini of all enterovirus genomes, comprising part of a cis-acting replication element essential for efficient enteroviral replication. 5' genomic terminal deletions up to as much as 55% of domain I can occur without lethality following coxsackie B virus infections. We report here that the entire CVB structural domain I can be deleted without lethality. |
Reversion to wildtype of a mutated and nonfunctional coxsackievirus B3CRE(2C).
Smithee S , Tracy S , Chapman NM . Virus Res 2016 220 136-49 The cis-acting replication element (CRE) in the 2C protein coding region [CRE(2C)] of enteroviruses (EV) facilitates the addition of two uridine residues (uridylylation) onto the virus-encoded protein VPg in order for it to serve as the RNA replication primer. We demonstrated that coxsackievirus B3 (CVB3) is replication competent in the absence of a native (uridylylating) CRE(2C) and also demonstrated that lack of a functional CRE(2C) led to generation of 5' terminal genomic deletions in the CVB3 CRE-knock-out (CVB3-CKO) population. We asked whether reversion of the mutated CRE(2C) occurred, thus permitting sustained replication, and when were 5' terminal deletions generated during replication. Virions were isolated from HeLa cells previously electroporated with infectious CVB3-CKO T7 transcribed RNA or from hearts and spleens of mice after transfection with CVB3-CKO RNA. Viral RNA was isolated in order to amplify the CRE(2C) coding region and the genomic 5' terminal sequences. Sequence analysis revealed reversion of the CVB3-CKO sequence to wildtype occurs by 8days post-electroporation of HeLa cells and by 20days post-transfection in mice. However, 5' terminal deletions evolve prior to these times. Reversion of the CRE(2C) mutations to wildtype despite loss of the genomic 5' termini is consistent with the hypothesis that an intact CRE(2C) is inherently vital to EV replication even when it is not enabling efficient positive strand initiation. |
Epidemiology of a large restaurant-associated outbreak of Shiga toxin-producing Escherichia coli O111:NM
Bradley KK , Williams JM , Burnsed LJ , Lytle MB , McDermott MD , Mody RK , Bhattarai A , Mallonee S , Piercefield EW , McDonald-Hamm CK , Smithee LK . Epidemiol Infect 2012 140 (9) 1644-54 SUMMARY: In August 2008, a large outbreak of Shiga toxin-producing Escherichia coli (STEC) O111:NM infections associated with a buffet-style restaurant in rural Oklahoma was identified. A case-control study of restaurant patrons and a retrospective cohort study of catered event attendees were conducted coupled with an environmental investigation to determine the outbreak's source and mode of transmission. Of 1823 persons interviewed, 341 (18.7%) met the outbreak case definition; 70 (20.5%) were hospitalized, 25 (7.3%) developed haemolytic uraemic syndrome, and one died. Multiple food items were significantly associated with illness by both bivariate and multivariate analyses, but none stood out as a predominant transmission vehicle. All water, food, and restaurant surface swabs, and stool cultures from nine ill employees were negative for the presence of Shiga toxin and E. coli O111:NM although epidemiological evidence suggested the outbreak resulted from cross-contamination of restaurant food from food preparation equipment or surfaces, or from an unidentified infected food handler. |
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