Last data update: Apr 29, 2024. (Total: 46658 publications since 2009)
Records 1-30 (of 44 Records) |
Query Trace: Roman W [original query] |
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Clinical Course of SARS-CoV-2 Infection in Adults with ESKD Receiving Outpatient Hemodialysis
Bardossy AC , Korhonen L , Schatzman S , Gable P , Herzig C , Brown NE , Beshearse E , Varela K , Sabour S , Lyons AK , Overton R , Hudson M , Hernandez-Romieu AC , Alvarez J , Roman K , Weng M , Soda E , Patel PR , Grate C , Dalrymple LS , Wingard RL , Thornburg NJ , Halpin ASL , Folster JM , Tobin-D'Angelo M , Lea J , Apata I , McDonald LC , Brown AC , Kutty PK , Novosad S . Kidney360 12/28/2021 2 (12) 1917-1927 BACKGROUND: Patients with ESKD on maintenance dialysis receive dialysis in common spaces with other patients and have a higher risk of severe SARS-CoV-2 infections. They may have persistently or intermittently positive SARS-CoV-2 RT-PCR tests after infection. We describe the clinical course of SARS-CoV-2 infection and the serologic response in a convenience sample of patients with ESKD to understand the duration of infectivity. METHODS: From August to November 2020, we enrolled patients on maintenance dialysis with SARS-CoV-2 infections from outpatient dialysis facilities in Atlanta, Georgia. We followed participants for approximately 42 days. We assessed COVID-19 symptoms and collected specimens. Oropharyngeal (OP), anterior nasal (AN), and saliva (SA) specimens were tested for the presence of SARS-CoV-2 RNA, using RT-PCR, and sent for viral culture. Serology, including neutralizing antibodies, was measured in blood specimens. RESULTS: Fifteen participants, with a median age of 58 (range, 37‒77) years, were enrolled. Median duration of RT-PCR positivity from diagnosis was 18 days (interquartile range [IQR], 8‒24 days). Ten participants had at least one, for a total of 41, positive RT-PCR specimens ≥10 days after symptoms onset. Of these 41 specimens, 21 underwent viral culture; one (5%) was positive 14 days after symptom onset. Thirteen participants developed SARS-CoV-2-specific antibodies, 11 of which included neutralizing antibodies. RT-PCRs remained positive after seroconversion in eight participants and after detection of neutralizing antibodies in four participants; however, all of these samples were culture negative. CONCLUSIONS: Patients with ESKD on maintenance dialysis remained persistently and intermittently SARS-CoV-2-RT-PCR positive. However, of the 15 participants, only one had infectious virus, on day 14 after symptom onset. Most participants mounted an antibody response, including neutralizing antibodies. Participants continued having RT-PCR-positive results in the presence of SARS-CoV-2-specific antibodies, but without replication-competent virus detected. |
Could less be more? Accounting for fractional-dose regimens and different number of vaccine doses when measuring the impact of the RTS, S/AS01E malaria vaccine
Westercamp N , Osei-Tutu L , Schuerman L , Kariuki SK , Bollaerts A , Lee CK , Samuels AM , Ockenhouse C , Bii DK , Adjei S , Oneko M , Lievens M , Attobrah Sarfo MA , Atieno C , Bakari A , Sang T , Kotoh-Mortty MF , Otieno K , Roman F , Buabeng PBY , Ntiamoah Y , Ansong D , Agbenyega T , Ofori-Anyinam O . J Infect Dis 2024 BACKGROUND: The RTS, S/AS01E malaria vaccine (RTS, S) is recommended for children in moderate-to-high Plasmodium falciparum malaria transmission areas. This phase 2b trial (NCT03276962) evaluates RTS, S fractional- and full-dose regimens in Ghana and Kenya. METHODS: 1500 children aged 5-17 months were randomised (1:1:1:1:1) to receive RTS, S or rabies control vaccine. RTS, S groups received two full RTS, S doses at month (M)0/M1 followed by either full (groups R012-20, R012-14-26) or fractional (1/5) doses (groups Fx012-14-26, Fx017-20-32). RESULTS: At M32 post-first dose, vaccine efficacy (VE) against clinical malaria (all episodes) ranged from 38% (R012-20; 95%CI: 24-49) to 53% (R012-14-26; 95%CI: 42-62). Vaccine impact estimates (cumulative number of malaria cases averted/1000 children vaccinated) were 1344 (R012-20), 2450 (R012-14-26), 2273 (Fx012-14-26), 2112 (Fx017-20-32). To account for differences in vaccine volume (fractional- versus full-dose), in a post-hoc analysis, we also estimated cases averted/1000 RTS, S full-dose equivalents: 336 (R012-20), 490 (R012-14-26), 874 (Fx012-14-26), 880 (Fx017-20-32). CONCLUSIONS: VE against clinical malaria was similar in all RTS, S groups. Vaccine impact accounting for full-dose equivalence suggests that using fractional-dose regimens could be a viable dose-sparing strategy. If borne out through trial end (M50), these observations underscore the means to reduce cost per regimen with a goal of maximising impact and optimising supply. |
Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases.
Arias A , Watson SJ , Asogun D , Tobin EA , Lu J , Phan MVT , Jah U , Wadoum REG , Meredith L , Thorne L , Caddy S , Tarawalie A , Langat P , Dudas G , Faria NR , Dellicour S , Kamara A , Kargbo B , Kamara BO , Gevao S , Cooper D , Newport M , Horby P , Dunning J , Sahr F , Brooks T , Simpson AJH , Groppelli E , Liu G , Mulakken N , Rhodes K , Akpablie J , Yoti Z , Lamunu M , Vitto E , Otim P , Owilli C , Boateng I , Okoror L , Omomoh E , Oyakhilome J , Omiunu R , Yemisis I , Adomeh D , Ehikhiametalor S , Akhilomen P , Aire C , Kurth A , Cook N , Baumann J , Gabriel M , Wölfel R , Di Caro A , Carroll MW , Günther S , Redd J , Naidoo D , Pybus OG , Rambaut A , Kellam P , Goodfellow I , Cotten M . Virus Evol 2016 2 (1) vew016 To end the largest known outbreak of Ebola virus disease (EVD) in West Africa and to prevent new transmissions, rapid epidemiological tracing of cases and contacts was required. The ability to quickly identify unknown sources and chains of transmission is key to ending the EVD epidemic and of even greater importance in the context of recent reports of Ebola virus (EBOV) persistence in survivors. Phylogenetic analysis of complete EBOV genomes can provide important information on the source of any new infection. A local deep sequencing facility was established at the Mateneh Ebola Treatment Centre in central Sierra Leone. The facility included all wetlab and computational resources to rapidly process EBOV diagnostic samples into full genome sequences. We produced 554 EBOV genomes from EVD cases across Sierra Leone. These genomes provided a detailed description of EBOV evolution and facilitated phylogenetic tracking of new EVD cases. Importantly, we show that linked genomic and epidemiological data can not only support contact tracing but also identify unconventional transmission chains involving body fluids, including semen. Rapid EBOV genome sequencing, when linked to epidemiological information and a comprehensive database of virus sequences across the outbreak, provided a powerful tool for public health epidemic control efforts. |
Role of pre-farrow natural planned exposure of gilts in shaping the passive antibody response to rotavirus a in piglets
Kumar D , Anderson Reever AV , Pittman JS , Springer NL , Mallen K , Roman-Sosa G , Sangewar N , Casey-Moore MC , Bowen MD , Mwangi W , Marthaler DG . Vaccines (Basel) 2023 11 (12) Natural planned exposure (NPE) remains one of the most common methods in swine herds to boost lactogenic immunity against rotaviruses. However, the efficacy of NPE protocols in generating lactogenic immunity has not been investigated before. A longitudinal study was conducted to investigate the dynamics of genotype-specific antibody responses to different doses (3, 2 and 1) of Rotavirus A (RVA) NPE (genotypes G4, G5, P[7] and P[23]) in gilts and the transfer of lactogenic immunity to their piglets. Group 1 gilts received three doses of NPE at 5, 4 and 3 weeks pre-farrow (WPF), group 2 received two doses at 5 and 3 WPF, group 3 received one dose at 5 WPF, and group 4 received no NPE (control group). VP7 (G4 and G5) and truncated VP4* (P[7] and P[23]) antigens of RVA were expressed in mammalian and bacterial expression systems, respectively, and used to optimize indirect ELISAs to determine antibody levels against RVA in gilts and piglets. In day-0 colostrum samples, group 1 had significantly higher IgG titers compared to the control group for all four antigens, and either significantly or numerically higher IgG titers than groups 2 and 3. Group 1 also had significantly higher colostrum IgA levels than the control group for all antigens (except G4), and either significantly or numerically higher IgA levels compared to groups 2 and 3. In piglet serum, group 1 piglets had higher IgG titers for all four antigens at day 0 than the other groups. Importantly, RVA NPE stimulated antibodies in all groups regardless of the treatment doses and prevented G4, G5, P[7] and P[23] RVA fecal shedding prior to weaning in piglets in the absence of viral challenge. The G11 and P[34] RVA genotypes detected from pre-weaning piglets differed at multiple amino acid positions with parent NPE strains. In conclusion, the results of this study suggest that the group 1 NPE regimen (three doses of NPE) resulted in the highest anti-RVA antibody (IgG and IgA) levels in the colostrum/milk, and the highest IgG levels in piglet serum. |
Identification of the flavivirus conserved residues in the envelope protein hinge region for the rational design of a candidate West Nile live-attenuated vaccine
Maloney BE , Carpio KL , Bilyeu AN , Saunders DRD , Park SL , Pohl AE , Ball NC , Raetz JL , Huang CY , Higgs S , Barrett ADT , Roman-Sosa G , Kenney JL , Vanlandingham DL , Huang YS . NPJ Vaccines 2023 8 (1) 172 The flavivirus envelope protein is a class II fusion protein that drives flavivirus-cell membrane fusion. The membrane fusion process is triggered by the conformational change of the E protein from dimer in the virion to trimer, which involves the rearrangement of three domains, EDI, EDII, and EDIII. The movement between EDI and EDII initiates the formation of the E protein trimer. The EDI-EDII hinge region utilizes four motifs to exert the hinge effect at the interdomain region and is crucial for the membrane fusion activity of the E protein. Using West Nile virus (WNV) NY99 strain derived from an infectious clone, we investigated the role of eight flavivirus-conserved hydrophobic residues in the EDI-EDII hinge region in the conformational change of E protein from dimer to trimer and viral entry. Single mutations of the E-A54, E-I130, E-I135, E-I196, and E-Y201 residues affected infectivity. Importantly, the E-A54I and E-Y201P mutations fully attenuated the mouse neuroinvasive phenotype of WNV. The results suggest that multiple flavivirus-conserved hydrophobic residues in the EDI-EDII hinge region play a critical role in the structure-function of the E protein and some contribute to the virulence phenotype of flaviviruses as demonstrated by the attenuation of the mouse neuroinvasive phenotype of WNV. Thus, as a proof of concept, residues in the EDI-EDII hinge region are proposed targets to engineer attenuating mutations for inclusion in the rational design of candidate live-attenuated flavivirus vaccines. |
Online solid phase extraction high-performance liquid chromatography - Isotope dilution - Tandem mass spectrometry quantification of organophosphate pesticides, synthetic pyrethroids, and selected herbicide metabolites in human urine
Wambua D , Roman W , Vidanage I , Vidal M , Calafat AM , Ospina M . Chemosphere 2023 340 139863 Analytical methods to quantify pesticide biomarkers in human population studies are critical for exposure assessment given the widespread use of pesticides for pest and weed control and their potential for affecting human health. We developed a method to quantify, in 0.2 mL of urine, concentrations of 10 pesticide biomarkers: four organophosphate insecticide metabolites (3,5,6-trichloro-2-pyridinol (TCPy), 2-isopropyl-6-methyl-4-pyrimidinol, para-nitrophenol, malathion dicarboxylic acid); five synthetic pyrethroid insecticide metabolites (4-fluoro-3-phenoxybenzoic acid, 3-phenoxybenzoic acid, cis and trans-3-(2,2-dichlorovinyl)-2,2-dimethylcyclopropane carboxylic acid (DCCA), cis-3-(2,2-dibromovinyl)-2,2-dimethylcyclopropane-1-carboxylic acid); and the herbicide 2,4-dichlorophenoxyacetic acid. The method is based on enzymatic hydrolysis of conjugated urinary metabolites, extraction and pre-concentration of the deconjugated metabolites using automated online solid-phase extraction, and separation and quantification using liquid chromatography-isotope dilution tandem mass spectrometry. Depending on the analyte, method detection limits were 0.1-0.6 ng/mL; mean accuracy, calculated as spike recoveries, was 91-102%, and total precision, given as percent variation coefficient, was 5.9-11.5%. Percent differences associated with three freeze-thaw cycles, 24-h benchtop storage, and short-term processed sample stability were <14%. METHOD: suitability was assessed by recurring successful participation in external quality assessment schemes and by analyzing samples from subjects with suspected exposure to pesticides (n = 40) or who self-reported consuming an organic diet (n = 50). Interquartile ranges were considerably lower for people consuming an organic diet than for those potentially exposed for cis-DCCA (0.37 ng/mL vs 0.75 ng/mL), trans-DCCA (0.88 ng/mL vs 1.78 ng/mL) and TCPy (1.81 ng/mL vs 2.48 ng/mL). This method requires one-fifth of the sample used in our previous method and is suitable for assessing background exposures to select pesticides in large human populations and for studies with limited sample volumes. |
Profiles of children with cortical visual impairment who use augmentative and alternative communication: A retrospective examination
Blackstone S , Luo F , Barker RM , Sevcik RA , Romski M , Casella V , Roman-Lantzy C . Am J Speech Lang Pathol 2022 31 (6) 2707-2721 PURPOSE: Cortical visual impairment (CVI) is the most common cause of visual impairment in children today and can impact the outcomes of children who rely on augmentative and alternative communication (AAC). This study provides baseline data of 13 children with CVI who used AAC during their first year of participation in an integrated CVI program. One purpose was to describe similarities and differences in the student's demographic, functional vision, communication, and educational profiles. A second purpose was to examine differences in students described with different communicator profiles. METHOD: Archived student records were de-identified and reviewed using a systematic coding scheme. Two researchers independently reviewed and coded all student records. Reliability was established. Measures included CVI Range scores; supports for positioning, mobility, vision, and writing; AAC systems, including modes, access methods, and language representation; communicative competence; self-determination; literacy; and mathematics. RESULTS: The study yielded a rich description of similarities and differences among students at baseline and led to careful consideration of differences among the participants with emergent communicator and context-dependent communicator profiles. CONCLUSIONS: Currently, limited evidence exists that informs practice regarding AAC assessment and intervention for children with CVI. This article describes a small sample of children with CVI who use AAC. Results underscore the need for educators and practitioners to ensure that vision functioning in students with CVI is evaluated carefully and regularly when conducting AAC assessment and intervention and formulating communication or education goals. SUPPLEMENTAL MATERIAL: https://doi.org/10.23641/asha.21357684. |
The Impact of Community-Based Testing Sites and Gift Incentives on COVID-19 Testing Uptake in Maryland, April 29 - May 9, 2021.
Turbyfill C , Thomas I , Agravat N , Prasher JM , Nett RJ , Stevens M , Ricaldi JN , Dunams TM , Brickhouse-Frazier L , Carter MD , Gebru Y , King A , May CS , Miller JD , Oguh C , Pullman A , Roman K , Rose C , Scherr R , Sidibe T , Soelaeman R , Weinstein J , Wilson T , Tran CH . Am J Health Promot 2022 37 (2) 8901171221119796 PURPOSE: Information on incentives for COVID-19 testing is needed to understand effective practices that encourage testing uptake. We describe characteristics of those who received an incentive after performing a rapid antigen test. DESIGN: Cross-sectional descriptive analysis of survey data. SETTING: During April 29-May 9, 2021, COVID-19 rapid antigen testing was offered in 2 Maryland cities. SAMPLE: Convenience sample of 553 adults (≥18 years) who tested and received an incentive; 93% consented to survey. MEASURES: Survey questions assessed reasons for testing, testing history, barriers, and demographics. ANALYSIS: Robust Poisson regressions were used to determine characteristic differences based on testing history and between participants who would re-test in the future without an incentive vs participants who would not. RESULTS: The most common reasons for testing were the desire to be tested (n = 280; 54%) and convenience of location (n = 146; 28%). Those motivated by an incentive to test (n = 110; 21%) were 5.83 times as likely to state they would not test again without an incentive, compared to those with other reasons for testing (95% CI: 2.67-12.72, P < .001). CRITICAL LIMITATIONS: No comparative study group. CONCLUSION: Results indicate internal motivation and convenience were prominent factors supporting testing uptake. Incentives may increase community testing participation, particularly among people who have never tested. Keywords COVID-19, pandemic, incentives, health behavior, community testing. |
Factors Associated with Delayed or Missed Second-Dose mRNA COVID-19 Vaccination among Persons >12 Years of Age, United States.
Meng L , Murthy NC , Murthy BP , Zell E , Saelee R , Irving M , Fast HE , Roman PC , Schiller A , Shaw L , Black CL , Gibbs-Scharf L , Harris L , Chorba T . Emerg Infect Dis 2022 28 (8) 1633-1641 To identify demographic factors associated with delaying or not receiving a second dose of the 2-dose primary mRNA COVID-19 vaccine series, we matched 323 million single Pfizer-BioNTech (https://www.pfizer.com) and Moderna (https://www.modernatx.com) COVID-19 vaccine administration records from 2021 and determined whether second doses were delayed or missed. We used 2 sets of logistic regression models to examine associated factors. Overall, 87.3% of recipients received a timely second dose (≤42 days between first and second dose), 3.4% received a delayed second dose (>42 days between first and second dose), and 9.4% missed the second dose. Persons more likely to have delayed or missed the second dose belonged to several racial/ethnic minority groups, were 18-39 years of age, lived in more socially vulnerable areas, and lived in regions other than the northeastern United States. Logistic regression models identified specific subgroups for providing outreach and encouragement to receive subsequent doses on time. |
Efficacy of RTS,S/AS01(E) malaria vaccine administered according to different full, fractional, and delayed third or early fourth dose regimens in children aged 5-17 months in Ghana and Kenya: an open-label, phase 2b, randomised controlled trial
Samuels AM , Ansong D , Kariuki SK , Adjei S , Bollaerts A , Ockenhouse C , Westercamp N , Lee CK , Schuerman L , Bii DK , Osei-Tutu L , Oneko M , Lievens M , Attobrah Sarfo MA , Atieno C , Morelle D , Bakari A , Sang T , Jongert E , Kotoh-Mortty MF , Otieno K , Roman F , Buabeng PBY , Ntiamoah Y , Ofori-Anyinam O , Agbenyega T . Lancet Infect Dis 2022 22 (9) 1329-1342 BACKGROUND: Controlled infection studies in malaria-naive adults suggest increased vaccine efficacy for fractional-dose versus full-dose regimens of RTS,S/AS01. We report first results of an ongoing trial assessing different fractional-dose regimens in children, in natural exposure settings. METHODS: This open-label, phase 2b, randomised controlled trial is conducted at the Malaria Research Center, Agogo, Ashanti Region (Ghana), and the Kenya Medical Research Institute and the US Centers for Disease Control and Prevention site in Siaya County (Kenya). We enrolled children aged 5-17 months without serious acute or chronic illness who had previously received three doses of diphtheria, tetanus, pertussis, and hepatitis B vaccine and at least three doses of oral polio vaccine. Children were randomly assigned (1:1:1:1:1) using a web-based randomisation system with a minimisation procedure accounting for centre to receive rabies control vaccine (M012 schedule) or two full doses of RTS,S/AS01(E) at month 0 and month 1, followed by either full doses at months 2 and 20 (group R012-20 [standard regimen]), full doses at months 2, 14, 26, and 38 (R012-14), fractional doses at months 2, 14, 26, and 38 (Fx012-14), or fractional doses at months 7, 20, and 32 (Fx017-20). The fractional doses were administered as one fifth (0·1 mL) of the full RTS,S dose (0·5 mL) after reconstitution. All vaccines were administered by intramuscular injection in the left deltoid. The primary outcome was occurrence of clinical malaria cases from month 2·5 until month 14 for the Fx012-14 group versus the pooled R012-14 and R012-20 groups in the per-protocol set. We assessed incremental vaccine efficacy of the Fx012-14 group versus the pooled R012-14 and R012-20 group over 12 months after dose three. Safety was assessed in all children who received at least one vaccine dose. This trial is registered with ClinicalTrials.gov, NCT03276962. FINDINGS: Between Sept 28, 2017, and Sept 25, 2018, 2157 children were enrolled, of whom 1609 were randomly assigned to a treatment group (322 to each RTS,S/AS01(E) group and 321 to the rabies vaccine control group). 1500 children received at least one study vaccine dose and the per-protocol set comprised 1332 children. Over 12 months after dose three, the incremental vaccine efficacy in the Fx012-14 group versus the pooled R012-14 and R12-20 groups was -21% (95% CI -57 to 7; p=0·15). Up to month 21, serious adverse events occurred in 48 (16%) of 298 children in the R012-20 group, 45 (15%) of 294 in the R012-14 group, 47 (15%) of 304 in the Fx012-14 group, 62 (20%) of 311 in the Fx017-20 group, and 71 (24%) of 293 in the control group, with no safety signals observed. INTERPRETATION: The Fx012-14 regimen was not superior to the standard regimen over 12 months after dose three. All RTS,S/AS01(E) regimens provided substantial, similar protection against clinical malaria, suggesting potential flexibility in the recommended dosing regimen and schedule. This, and the effect of annual boosters, will be further evaluated through 50 months of follow-up. FUNDING: GlaxoSmithKline Biologicals; PATH's Malaria Vaccine Initiative. |
Disparities in COVID-19 Vaccination Coverage Between Urban and Rural Counties - United States, December 14, 2020-January 31, 2022.
Saelee R , Zell E , Murthy BP , Castro-Roman P , Fast H , Meng L , Shaw L , Gibbs-Scharf L , Chorba T , Harris LQ , Murthy N . MMWR Morb Mortal Wkly Rep 2022 71 (9) 335-340 Higher COVID-19 incidence and mortality rates in rural than in urban areas are well documented (1). These disparities persisted during the B.1.617.2 (Delta) and B.1.1.529 (Omicron) variant surges during late 2021 and early 2022 (1,2). Rural populations tend to be older (aged 65 years) and uninsured and are more likely to have underlying medical conditions and live farther from facilities that provide tertiary medical care, placing them at higher risk for adverse COVID-19 outcomes (2). To better understand COVID-19 vaccination disparities between urban and rural populations, CDC analyzed county-level vaccine administration data among persons aged 5 years who received their first dose of either the BNT162b2 (Pfizer-BioNTech) or mRNA-1273 (Moderna) COVID-19 vaccine or a single dose of the Ad.26.COV2.S (Janssen [Johnson & Johnson]) COVID-19 vaccine during December 14, 2020-January 31, 2022, in 50 states and the District of Columbia (DC). COVID-19 vaccination coverage with 1 doses in rural areas (58.5%) was lower than that in urban counties (75.4%) overall, with similar patterns across age groups and sex. Coverage with 1 doses varied among states: 46 states had higher coverage in urban than in rural counties, one had higher coverage in rural than in urban counties. Three states and DC had no rural counties; thus, urban-rural differences could not be assessed. COVID-19 vaccine primary series completion was higher in urban than in rural counties. However, receipt of booster or additional doses among primary series recipients was similarly low between urban and rural counties. Compared with estimates from a previous study of vaccine coverage among adults aged 18 years during December 14, 2020-April 10, 2021, these urban-rural disparities among those now eligible for vaccination (aged 5 years) have increased more than twofold through January 2022, despite increased availability and access to COVID-19 vaccines. Addressing barriers to vaccination in rural areas is critical to achieving vaccine equity, reducing disparities, and decreasing COVID-19-related illness and death in the United States (2). |
Pregnancy Risk Assessment Monitoring System for Dads: A piloted randomized trial of public health surveillance of recent fathers' behaviors before and after infant birth
Garfield CF , Simon CD , Stephens F , Castro Román P , Bryan M , Smith RA , Kortsmit K , Salvesen von Essen B , Williams L , Kapaya M , Dieke A , Barfield W , Warner L . PLoS One 2022 17 (1) e0262366 BACKGROUND: Becoming a father impacts men's health and wellbeing, while also contributing to the health and wellbeing of mothers and children. There is no large-scale, public health surveillance system aimed at understanding the health and behaviors of men transitioning into fatherhood. The purpose of this study was to describe piloted randomized approaches of a state-based surveillance system examining paternal behaviors before and after their infant's birth to better understand the health needs of men and their families during the transition to parenthood. METHODS: During October 2018-July 2019, 857 fathers in Georgia were sampled 2-6 months after their infant's birth from birth certificates files and surveyed via mail, online or telephone, in English or Spanish, using two randomized approaches: Indirect-to-Dads and Direct-to-Dads. Survey topics included mental and physical health, healthcare, substance use, and contraceptive use. FINDINGS: Weighted response rates (Indirect-to-Dads, 33%; Direct-to-Dads, 31%) and population demographics did not differ by approach. Respondents completed the survey by mail (58%), online (28%) or telephone (14%). Among 266 fathers completing the survey, 55% had a primary care physician, and 49% attended a healthcare visit for themselves during their infant's mother's pregnancy or since their infant's birth. Most fathers were overweight or had obesity (70%) while fewer reported smoking cigarettes (19%), binge drinking (13%) or depressive symptoms (10%) since their infant's birth. CONCLUSIONS: This study tests a novel approach for obtaining population-based estimates of fathers' perinatal health behaviors, with comparable response rates from two pragmatic approaches. The pilot study results quantify a number of public health needs related to fathers' health and healthcare access. |
Influenza Vaccinations During the COVID-19 Pandemic - 11 U.S. Jurisdictions, September-December 2020.
Roman PC , Kirtland K , Zell ER , Jones-Jack N , Shaw L , Shrader L , Sprague C , Schultz J , Le Q , Nalla A , Kuramoto S , Cheng I , Woinarowicz M , Robison S , Robinson S , Meder K , Murphy A , Gibbs-Scharf L , Harris L , Murthy BP . MMWR Morb Mortal Wkly Rep 2021 70 (45) 1575-1578 Influenza causes considerable morbidity and mortality in the United States. Between 2010 and 2020, an estimated 9-41 million cases resulted in 140,000-710,000 hospitalizations and 12,000-52,000 deaths annually (1). As the United States enters the 2021-22 influenza season, the potential impact of influenza illnesses is of concern given that influenza season will again coincide with the ongoing COVID-19 pandemic, which could further strain overburdened health care systems. The Advisory Committee on Immunization Practices (ACIP) recommends routine annual influenza vaccination for the 2021-22 influenza season for all persons aged ≥6 months who have no contraindications (2). To assess the potential impact of the COVID-19 pandemic on influenza vaccination coverage, the percentage change between administration of at least 1 dose of influenza vaccine during September-December 2020 was compared with the average administered in the corresponding periods in 2018 and 2019. The data analyzed were reported from 11 U.S. jurisdictions with high-performing state immunization information systems.* Overall, influenza vaccine administration was 9.0% higher in 2020 compared with the average in 2018 and 2019, combined. However, in 2020, the number of influenza vaccine doses administered to children aged 6-23 months and children aged 2-4 years, was 13.9% and 11.9% lower, respectively than the average for each age group in 2018 and 2019. Strategic efforts are needed to ensure high influenza vaccination coverage among all age groups, especially children aged 6 months-4 years who are not yet eligible to receive a COVID-19 vaccine. Administration of influenza vaccine and a COVID-19 vaccine among eligible populations is especially important to reduce the potential strain that influenza and COVID-19 cases could place on health care systems already overburdened by COVID-19. |
Antibodies to SARS-CoV-2 in All of Us Research Program Participants, January 2-March 18, 2020.
Althoff KN , Schlueter DJ , Anton-Culver H , Cherry J , Denny JC , Thomsen I , Karlson EW , Havers FP , Cicek MS , Thibodeau SN , Pinto LA , Lowy D , Malin BA , Ohno-Machado L , Williams C , Goldstein D , Kouame A , Ramirez A , Roman A , Sharpless NE , Gebo KA , Schully SD . Clin Infect Dis 2021 74 (4) 584-590 BACKGROUND: With limited SARS-CoV-2 testing capacity in the US at the start of the epidemic (January - March), testing was focused on symptomatic patients with a travel history throughout February, obscuring the picture of SARS-CoV-2 seeding and community transmission. We sought to identify individuals with SARS-CoV-2 antibodies in the early weeks of the US epidemic. METHODS: All of Us study participants in all 50 US states provided blood specimens during study visits from January 2 to March 18, 2020. A participant was considered seropositive if they tested positive for SARS-CoV-2 immunoglobulin G (IgG) antibodies on the Abbott Architect SARS-CoV-2 IgG ELISA and the EUROIMMUN SARS-CoV-2 ELISA in a sequential testing algorithm. Sensitivity and specificity of the Abbott and EUROIMMUNE ELISAs and the net sensitivity and specificity of the sequential testing algorithm were estimated with 95% confidence intervals. RESULTS: The estimated sensitivity of Abbott and EUROIMMUN was 100% (107/107 [96.6%, 100%]) and 90.7% (97/107 [83.5%, 95.4%]), respectively. The estimated specificity of Abbott and EUROIMMUN was 99.5% (995/1,000 [98.8%, 99.8%]) and 99.7% (997/1,000 [99.1%, 99.9%), respectively. The net sensitivity and specificity of our sequential testing algorithm was 90.7% (97/107 [83.5%, 95.4%]) and 100.0% (1,000/1,000 [99.6%, 100%]), respectively. Of the 24,079 study participants with blood specimens from January 2 to March 18, 2020, 9 were seropositive, 7 of whom were seropositive prior to the first confirmed case in the states of Illinois, Massachusetts, Wisconsin, Pennsylvania, and Mississippi. CONCLUSIONS: Our findings indicate SARS-CoV-2 infections weeks prior to the first recognized cases in 5 US states. |
Performance of a fully-automated system on a WHO malaria microscopy evaluation slide set.
Horning MP , Delahunt CB , Bachman CM , Luchavez J , Luna C , Hu L , Jaiswal MS , Thompson CM , Kulhare S , Janko S , Wilson BK , Ostbye T , Mehanian M , Gebrehiwot R , Yun G , Bell D , Proux S , Carter JY , Oyibo W , Gamboa D , Dhorda M , Vongpromek R , Chiodini PL , Ogutu B , Long EG , Tun K , Burkot TR , Lilley K , Mehanian C . Malar J 2021 20 (1) 110 BACKGROUND: Manual microscopy remains a widely-used tool for malaria diagnosis and clinical studies, but it has inconsistent quality in the field due to variability in training and field practices. Automated diagnostic systems based on machine learning hold promise to improve quality and reproducibility of field microscopy. The World Health Organization (WHO) has designed a 55-slide set (WHO 55) for their External Competence Assessment of Malaria Microscopists (ECAMM) programme, which can also serve as a valuable benchmark for automated systems. The performance of a fully-automated malaria diagnostic system, EasyScan GO, on a WHO 55 slide set was evaluated. METHODS: The WHO 55 slide set is designed to evaluate microscopist competence in three areas of malaria diagnosis using Giemsa-stained blood films, focused on crucial field needs: malaria parasite detection, malaria parasite species identification (ID), and malaria parasite quantitation. The EasyScan GO is a fully-automated system that combines scanning of Giemsa-stained blood films with assessment algorithms to deliver malaria diagnoses. This system was tested on a WHO 55 slide set. RESULTS: The EasyScan GO achieved 94.3 % detection accuracy, 82.9 % species ID accuracy, and 50 % quantitation accuracy, corresponding to WHO microscopy competence Levels 1, 2, and 1, respectively. This is, to our knowledge, the best performance of a fully-automated system on a WHO 55 set. CONCLUSIONS: EasyScan GO's expert ratings in detection and quantitation on the WHO 55 slide set point towards its potential value in drug efficacy use-cases, as well as in some case management situations with less stringent species ID needs. Improved runtime may enable use in general case management settings. |
Environmental contamination of contact precaution and non-contact precaution patient rooms in six acute care facilities
Tanner WD , Leecaster MK , Zhang Y , Stratford KM , Mayer J , Visnovsky LD , Alhmidi H , Cadnum JL , Jencson AL , Koganti S , Bennett CP , Donskey CJ , Noble-Wang J , Reddy SC , Rose LJ , Watson L , Ide E , Wipperfurth T , Safdar N , Arasim M , Macke C , Roman P , Krein SL , Loc-Carrillo C , Samore MH . Clin Infect Dis 2021 72 S8-s16 BACKGROUND: Environmental contamination is an important source of hospital multidrug-resistant organism (MDRO) transmission. Factors such as patient MDRO contact precautions (CP) status, patient proximity to surfaces, and unit type likely influence MDRO contamination and bacterial bioburden levels on patient room surfaces. Identifying factors associated with environmental contamination in patient rooms and on shared unit surfaces could help identify important environmental MDRO transmission routes. METHODS: Surfaces were sampled from MDRO CP and non-CP rooms, nursing stations, and mobile equipment in acute care, intensive care, and transplant units within 6 acute care hospitals using a convenience sampling approach blinded to cleaning events. Precaution rooms had patients with clinical or surveillance tests positive for methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci, carbapenem-resistant Enterobacteriaceae or Acinetobacter within the previous 6 months, or Clostridioides difficile toxin within the past 30 days. Rooms not meeting this definition were considered non-CP rooms. Samples were cultured for the above MDROs and total bioburden. RESULTS: Overall, an estimated 13% of rooms were contaminated with at least 1 MDRO. MDROs were detected more frequently in CP rooms (32% of 209 room-sample events) than non-CP rooms (12% of 234 room-sample events). Surface bioburden did not differ significantly between CP and non-CP rooms or MDRO-positive and MDRO-negative rooms. CONCLUSIONS: CP room surfaces are contaminated more frequently than non-CP room surfaces; however, contamination of non-CP room surfaces is not uncommon and may be an important reservoir for ongoing MDRO transmission. MDRO contamination of non-CP rooms may indicate asymptomatic patient MDRO carriage, inadequate terminal cleaning, or cross-contamination of room surfaces via healthcare personnel hands. |
Human Calicivirus Typing tool: A web-based tool for genotyping human norovirus and sapovirus sequences.
Tatusov RL , Chhabra P , Diez-Valcarce M , Barclay L , Cannon JL , Vinjé J . J Clin Virol 2020 134 104718 BACKGROUND: The family Caliciviridae consists of a genetically diverse group of RNA viruses that infect a wide range of host species including noroviruses and sapoviruses which cause acute gastroenteritis in humans. Typing of these viruses relies on sequence-based approaches, and therefore there is a need for rapid and accurate web-based typing tools. OBJECTIVE: To develop and evaluate a web-based tool for rapid and accurate genotyping of noroviruses and sapoviruses. METHODS: The Human Calicivirus Typing (HuCaT) tool uses a set of curated reference sequences that are compared to query sequences using a k-mer (DNA substring) based algorithm. Outputs include alignments and phylogenetic trees of the 12 top matching reference sequences for each query. RESULTS: The HuCaT tool was validated with a set of 1310 norovirus and 239 sapovirus sequences covering all known human norovirus and sapovirus genotypes. HuCaT tool assigned genotypes to all queries with 100 % accuracy and was much faster (17 s) than BLAST (150 s) or phylogenetic analyses approaches. CONCLUSIONS: The web-based HuCaT tool supports rapid and accurate genotyping of human noroviruses and sapoviruses. |
Measuring the efficacy of a pilot public health intervention for engaging communities of Puerto Rico to rapidly write hurricane protection plans
Keim ME , Runnels LA , Lovallo AP , Pagan Medina M , Roman Rosa E , Ramery Santos M , Mahany M , Cruz MA . Prehosp Disaster Med 2020 36 (1) 1-10 OBJECTIVE: The efficacy is measured for a public health intervention related to community-based planning for population protection measures (PPMs; ie, shelter-in-place and evacuation). DESIGN: This is a mixed (qualitative and quantitative) prospective study of intervention efficacy, measured in terms of usability related to effectiveness, efficiency, satisfaction, and degree of community engagement. SETTING: Two municipalities in the Commonwealth of Puerto Rico are included. PARTICIPANTS: Community members consisting of individuals; traditional leaders; federal, territorial, and municipal emergency managers; municipal mayors; National Guard; territorial departments of education, health, housing, public works, and transportation; health care; police; Emergency Medical Services; faith-based organizations; nongovernmental organizations (NGOs); and the private sector. INTERVENTION: The intervention included four community convenings: one for risk communication; two for plan-writing; and one tabletop exercise (TTX). This study analyzed data collected from the project work plan; participant rosters; participant surveys; workshop outputs; and focus group interviews. MAIN OUTCOME MEASURES: Efficacy was measured in terms of ISO 9241-11, an international standard for usability that includes effectiveness, efficiency, user satisfaction, and "freedom from risk" among users. Degree of engagement was considered an indicator of "freedom from risk," measurable through workshop attendance. RESULTS: Two separate communities drafted and exercised ~60-page-long population protection plans, each within 14.5 hours. Plan-writing workshops completed 100% of plan objectives and activities. Efficiency rates were nearly the same in both communities. Interviews and surveys indicated high degrees of community satisfaction. Engagement was consistent among community members and variable among governmental officials. CONCLUSIONS: Frontline communities have successfully demonstrated the ability to understand the environmental health hazards in their own community; rapidly write consensus-based plans for PPMs; participate in an objective-based TTX; and perform these activities in a bi-lingual setting. This intervention appears to be efficacious for public use in the rapid development of community-based PPMs. |
High levels of pretreatment and acquired HIV drug resistance in Nicaragua: results from the first nationally representative survey, 2016
Giron-Callejas A , Garcia-Morales C , Mendizabal-Burastero R , Roman M , Tapia-Trejo D , Perez-Garcia M , Quiroz-Morales VS , Juarez SI , Ravasi G , Vargas C , Gutierrez R , Romero L , Solorzano A , Sajquim E , Northbrook S , Avila-Rios S , Reyes-Teran G . J Int AIDS Soc 2019 22 (12) e25429 INTRODUCTION: A nationally representative HIV drug resistance (HIVDR) survey in Nicaragua was conducted to estimate the prevalence of pretreatment HIVDR (PDR) among antiretroviral therapy (ART) initiators and acquired HIVDR among people living with HIV (PLHIV) who had received ART for 12 +/- 3 months (ADR12) and >/=48 months (ADR48). METHODS: A nationwide cross-sectional survey with a two-stage cluster sampling was conducted from March to November 2016. Nineteen of 45 total ART clinics representing >90% of the national cohort of adults on ART were included. ART initiators were defined as PLHIV initiating or reinitiating first-line ART. HIVDR was assessed for protease, reverse transcriptase and integrase Sanger sequences using the Stanford HIVdb algorithm. Viral load (VL) suppression was defined as <1000 copies/mL. Results were weighted according to the survey design. RESULTS AND DISCUSSION: A total of 638 participants were enrolled (PDR: 171; ADR12: 114; ADR48: 353). The proportion of ART initiators with prior exposure to antiretrovirals (ARVs) was 12.3% (95% CI: 5.8% to 24.3%). PDR prevalence to any drug was 23.4% (95% CI: 14.4% to 35.6%), and 19.3% (95% CI: 12.2% to 29.1%) to non-nucleoside reverse transcriptase inhibitors (NNRTI). NNRTI PDR was higher in ART initiators with previous ARV exposure compared with those with no exposure (76.2% vs. 11.0%, p < 0.001). Protease inhibitors (PI) and integrase strand transfer inhibitors PDR was not observed. VL suppression rate was 77.8% (95% CI: 67.1% to 85.8%) in ADR12 and 70.3% (95% CI: 66.7% to 73.8%) in ADR48. ADR12 prevalence to any drug among PLHIV without VL suppression was 85.1% (95% CI: 66.1% to 94.4%), 82.4% to NNRTI and 70.2% to nucleoside reverse transcriptase inhibitors (NRTI). ADR48 prevalence to any drug among PLHIV without VL suppression was 75.5% (95% CI: 63.5% to 84.5 %), 70.7% to NNRTI, 59.4% to NRTI and 4.6% to PI. CONCLUSIONS: Despite implementation challenges yielding low-precision HIVDR estimates, high rates of NNRTI PDR were observed in Nicaragua, suggesting consideration of non-NNRTI-based first-line regimens for ART initiators. Strengthened HIVDR monitoring, systematic VL testing, and improved ART adherence support are also warranted. |
Determinants of uptake of intermittent preventive treatment during pregnancy: a review
Roman E , Andrejko K , Wolf K , Henry M , Youll S , Florey L , Ferenchick E , Gutman JR . Malar J 2019 18 (1) 372 Malaria in pregnancy (MiP) contributes to devastating maternal and neonatal outcomes. Coverage of intermittent preventive treatment during pregnancy (IPTp) remains alarmingly low. Data was compiled from MiP programme reviews and performed a literature search on access to and determinants of IPTp. National malaria control and reproductive health (RH) policies may be discordant. Integration may improve coverage. Medication stock-outs are a persistent problem. Quality improvement programmes are often not standardized. Capacity building varies across countries. Community engagement efforts primarily focus on promotion of services. The majority of challenges can be addressed at country level to improve IPTp coverage. |
Emerging Novel GII.P16 Noroviruses Associated with Multiple Capsid Genotypes.
Barclay L , Cannon JL , Wikswo ME , Phillips AR , Browne H , Montmayeur AM , Tatusov RL , Burke RM , Hall AJ , Vinje J . Viruses 2019 11 (6) Noroviruses evolve by antigenic drift and recombination, which occurs most frequently at the junction between the non-structural and structural protein coding genomic regions. In 2015, a novel GII.P16-GII.4 Sydney recombinant strain emerged, replacing the predominance of GII.Pe-GII.4 Sydney among US outbreaks. Distinct from GII.P16 polymerases detected since 2010, this novel GII.P16 was subsequently detected among GII.1, GII.2, GII.3, GII.10 and GII.12 viruses, prompting an investigation on the unique characteristics of these viruses. Norovirus positive samples (n = 1807) were dual-typed, of which a subset (n = 124) was sequenced to yield near-complete genomes. CaliciNet and National Outbreak Reporting System (NORS) records were matched to link outbreak characteristics and case outcomes to molecular data and GenBank was mined for contextualization. Recombination with the novel GII.P16 polymerase extended GII.4 Sydney predominance and increased the number of GII.2 outbreaks in the US. Introduction of the novel GII.P16 noroviruses occurred without unique amino acid changes in VP1, more severe case outcomes, or differences in affected population. However, unique changes were found among NS1/2, NS4 and VP2 proteins, which have immune antagonistic functions, and the RdRp. Multiple polymerase-capsid combinations were detected among GII viruses including 11 involving GII.P16. Molecular surveillance of protein sequences from norovirus genomes can inform the functional importance of amino acid changes in emerging recombinant viruses and aid in vaccine and antiviral formulation. |
Near-Complete Human Sapovirus Genome Sequences from Kenya.
Diez-Valcarce M , Montmayeur A , Tatusov R , Vinje J . Microbiol Resour Announc 2019 8 (7) We report five near-complete sapovirus genome sequences, including GI.3, GII.2, and GII.6 and two novel GII.NA (not assigned) strains. These new sequences expand the collection of human sapoviruses, allowing for a more accurate phylogenetic analysis of circulating strains and for designing broadly reactive primers for their detection and typing. |
Nonhuman primates across sub-Saharan Africa are infected with the yaws bacterium Treponema pallidum subsp. pertenue.
Knauf S , Gogarten JF , Schuenemann VJ , De Nys HM , Dux A , Strouhal M , Mikalova L , Bos KI , Armstrong R , Batamuzi EK , Chuma IS , Davoust B , Diatta G , Fyumagwa RD , Kazwala RR , Keyyu JD , Lejora IAV , Levasseur A , Liu H , Mayhew MA , Mediannikov O , Raoult D , Wittig RM , Roos C , Leendertz FH , Smajs D , Nieselt K , Krause J , Calvignac-Spencer S . Emerg Microbes Infect 2018 7 (1) 157 The bacterium Treponema pallidum (TP) causes human syphilis (subsp. pallidum; TPA), bejel (subsp. endemicum; TEN), and yaws (subsp. pertenue; TPE)1. Although syphilis has reached a worldwide distribution2, bejel and yaws have remained endemic diseases. Bejel affects individuals in dry areas of Sahelian Africa and Saudi Arabia, whereas yaws affects those living in the humid tropics1. Yaws is currently reported as endemic in 14 countries, and an additional 84 countries have a known history of yaws but lack recent epidemiological data3,4. Although this disease was subject to global eradication efforts in the mid-20th century, it later reemerged in West Africa, Southern Asia, and the Pacific region5. New large-scale treatment options triggered the ongoing second eradication campaign, the goal of which is to eradicate yaws globally by 20205. |
Vital signs: Zika-associated birth defects and neurodevelopmental abnormalities possibly associated with congenital Zika virus infection - U.S. Territories and freely associated states, 2018
Rice ME , Galang RR , Roth NM , Ellington SR , Moore CA , Valencia-Prado M , Ellis EM , Tufa AJ , Taulung LA , Alfred JM , Perez-Padilla J , Delgado-Lopez CA , Zaki SR , Reagan-Steiner S , Bhatnagar J , Nahabedian JF 3rd , Reynolds MR , Yeargin-Allsopp M , Viens LJ , Olson SM , Jones AM , Baez-Santiago MA , Oppong-Twene P , VanMaldeghem K , Simon EL , Moore JT , Polen KD , Hillman B , Ropeti R , Nieves-Ferrer L , Marcano-Huertas M , Masao CA , Anzures EJ , Hansen RL Jr , Perez-Gonzalez SI , Espinet-Crespo CP , Luciano-Roman M , Shapiro-Mendoza CK , Gilboa SM , Honein MA . MMWR Morb Mortal Wkly Rep 2018 67 (31) 858-867 INTRODUCTION: Zika virus infection during pregnancy causes serious birth defects and might be associated with neurodevelopmental abnormalities in children. Early identification of and intervention for neurodevelopmental problems can improve cognitive, social, and behavioral functioning. METHODS: Pregnancies with laboratory evidence of confirmed or possible Zika virus infection and infants resulting from these pregnancies are included in the U.S. Zika Pregnancy and Infant Registry (USZPIR) and followed through active surveillance methods. This report includes data on children aged >/=1 year born in U.S. territories and freely associated states. Receipt of reported follow-up care was assessed, and data were reviewed to identify Zika-associated birth defects and neurodevelopmental abnormalities possibly associated with congenital Zika virus infection. RESULTS: Among 1,450 children of mothers with laboratory evidence of confirmed or possible Zika virus infection during pregnancy and with reported follow-up care, 76% had developmental screening or evaluation, 60% had postnatal neuroimaging, 48% had automated auditory brainstem response-based hearing screen or evaluation, and 36% had an ophthalmologic evaluation. Among evaluated children, 6% had at least one Zika-associated birth defect identified, 9% had at least one neurodevelopmental abnormality possibly associated with congenital Zika virus infection identified, and 1% had both. CONCLUSION: One in seven evaluated children had a Zika-associated birth defect, a neurodevelopmental abnormality possibly associated with congenital Zika virus infection, or both reported to the USZPIR. Given that most children did not have evidence of all recommended evaluations, additional anomalies might not have been identified. Careful monitoring and evaluation of children born to mothers with evidence of Zika virus infection during pregnancy is essential for ensuring early detection of possible disabilities and early referral to intervention services. |
A renewed focus on preventing malaria in pregnancy
Ferenchick EK , Roman E , Wolf K , Florey L , Youll S , Mangiaterra V , Agarwal K , Gutman J . Reprod Health 2018 15 (1) 131 While much progress has been achieved globally in the fight against malaria, the significant financial investments made to date have not translated into scaled-up malaria in pregnancy (MiP) prevention efforts. Mothers and newborns remain at risk, and now is the time to refocus efforts. Against the backdrop of a new global health architecture embodied by the principles of Every Women, Every Child and driven by the work of the H6 Partnership, Global Financing Facility, strong bilaterals and key financiers, there is a new and timely juncture to advocate for MiP. Recent updates in the WHO Recommendations on Antenatal Care for a Positive Pregnancy Experience present an opportunity to strengthen MiP as a core maternal and child health issue and position MiP prevention as a priority. |
An American Thoracic Society/National Heart, Lung, and Blood Institute Workshop Report: Addressing respiratory health equality in the United States
Celedon JC , Burchard EG , Schraufnagel D , Castillo-Salgado C , Schenker M , Balmes J , Neptune E , Cummings KJ , Holguin F , Riekert KA , Wisnivesky JP , Garcia JGN , Roman J , Kittles R , Ortega VE , Redline S , Mathias R , Thomas A , Samet J , Ford JG . Ann Am Thorac Soc 2017 14 (5) 814-826 Health disparities related to race, ethnicity, and socioeconomic status persist and are commonly encountered by practitioners of pediatric and adult pulmonary, critical care, and sleep medicine in the United States. To address such disparities and thus progress toward equality in respiratory health, the American Thoracic Society and the National Heart, Lung, and Blood Institute convened a workshop in May of 2015. The workshop participants addressed health disparities by focusing on six topics, each of which concluded with a panel discussion that proposed recommendations for research on racial, ethnic, and socioeconomic disparities in pulmonary, critical care, and sleep medicine. Such recommendations address best practices to advance research on respiratory health disparities (e.g., characterize broad ethnic groups into subgroups known to differ with regard to a disease of interest), risk factors for respiratory health disparities (e.g., study the impact of new tobacco or nicotine products on respiratory diseases in minority populations), addressing equity in access to healthcare and quality of care (e.g., conduct longitudinal studies of the impact of the Affordable Care Act on respiratory and sleep disorders), the impact of personalized medicine on disparities research (e.g., implement large studies of pharmacogenetics in minority populations), improving design and methodology for research studies in respiratory health disparities (e.g., use study designs that reduce participants' burden and foster trust by engaging participants as decision-makers), and achieving equity in the pulmonary, critical care, and sleep medicine workforce (e.g., develop and maintain robust mentoring programs for junior faculty, including local and external mentors). Addressing these research needs should advance efforts to reduce, and potentially eliminate, respiratory, sleep, and critical care disparities in the United States. |
Complexity and biosemiotics in evolutionary ecology of zoonotic infectious agents.
Kosoy M , Kosoy R . Evol Appl 2017 11 (4) 394-403 More is not automatically better. Generation and accumulation of information reflecting the complexity of zoonotic diseases as ecological systems do not necessarily lead to improved interpretation of the obtained information and understanding of these complex systems. The traditional conceptual framework for analysis of diseases ecology is neither designed for, nor adaptable enough, to absorb the mass of diverse sources of relevant information. The multidirectional and multidimensional approaches to analyses form an inevitable part in defining a role of zoonotic pathogens and animal hosts considering the complexity of their inter-relations. And the more data we have, the more involved the interpretation needs to be. The keyword for defining the roles of microbes as pathogens, animals as hosts, and environmental parameters as infection drivers is "functional importance." Microbes can act as pathogens toward their host only if/when they recognize the animal organism as the target. The same is true when the host recognizes the microbe as a pathogen rather than harmless symbiont based on the context of its occurrence in that host. Here, we propose conceptual tools developed in the realm of the interdisciplinary sciences of complexity and biosemiotics for extending beyond the currently dominant mindset in ecology and evolution of infectious diseases. We also consider four distinct hierarchical levels of perception guiding how investigators can approach zoonotic agents, as a subject of their research, representing differences in emphasizing particular elements and their relations versus more unified systemic approaches. |
Virus genomes reveal factors that spread and sustained the Ebola epidemic.
Dudas G , Carvalho LM , Bedford T , Tatem AJ , Baele G , Faria NR , Park DJ , Ladner JT , Arias A , Asogun D , Bielejec F , Caddy SL , Cotten M , D'Ambrozio J , Dellicour S , Caro AD , Diclaro JW , Duraffour S , Elmore MJ , Fakoli LS , Faye O , Gilbert ML , Gevao SM , Gire S , Gladden-Young A , Gnirke A , Goba A , Grant DS , Haagmans BL , Hiscox JA , Jah U , Kugelman JR , Liu D , Lu J , Malboeuf CM , Mate S , Matthews DA , Matranga CB , Meredith LW , Qu J , Quick J , Pas SD , Phan MV , Pollakis G , Reusken CB , Sanchez-Lockhart M , Schaffner SF , Schieffelin JS , Sealfon RS , Simon-Loriere E , Smits SL , Stoecker K , Thorne L , Tobin EA , Vandi MA , Watson SJ , West K , Whitmer S , Wiley MR , Winnicki SM , Wohl S , Wolfel R , Yozwiak NL , Andersen KG , Blyden SO , Bolay F , Carroll MW , Dahn B , Diallo B , Formenty P , Fraser C , Gao GF , Garry RF , Goodfellow I , Gunther S , Happi CT , Holmes EC , Kargbo B , Keita S , Kellam P , Koopmans MP , Kuhn JH , Loman NJ , Magassouba N , Naidoo D , Nichol ST , Nyenswah T , Palacios G , Pybus OG , Sabeti PC , Sall A , Stroher U , Wurie I , Suchard MA , Lemey P , Rambaut A . Nature 2017 544 (7650) 309-315 The 2013-2016 West African epidemic caused by the Ebola virus was of unprecedented magnitude, duration and impact. Here we reconstruct the dispersal, proliferation and decline of Ebola virus throughout the region by analysing 1,610 Ebola virus genomes, which represent over 5% of the known cases. We test the association of geography, climate and demography with viral movement among administrative regions, inferring a classic 'gravity' model, with intense dispersal between larger and closer populations. Despite attenuation of international dispersal after border closures, cross-border transmission had already sown the seeds for an international epidemic, rendering these measures ineffective at curbing the epidemic. We address why the epidemic did not spread into neighbouring countries, showing that these countries were susceptible to substantial outbreaks but at lower risk of introductions. Finally, we reveal that this large epidemic was a heterogeneous and spatially dissociated collection of transmission clusters of varying size, duration and connectivity. These insights will help to inform interventions in future epidemics. |
High-Throughput Next Generation Sequencing of Polioviruses.
Montmayeur AM , Ng TF , Schmidt A , Zhao K , Magana L , Iber J , Castro CJ , Chen Q , Henderson E , Ramos E , Shaw J , Tatusov RL , Dybdahl-Sissoko N , Endegue-Zanga MC , Adeniji JA , Oberste MS , Burns CC . J Clin Microbiol 2016 55 (2) 606-615 Poliovirus (PV) is currently targeted for worldwide eradication and containment. Sanger-based sequencing of the VP1 capsid region is the current standard method for PV surveillance; however, the whole genome sequence is sometimes needed for higher resolution global surveillance. In this study, we optimized whole genome sequencing protocols for poliovirus isolates and FTA cards using NGS, aiming for high sequence coverage, efficiency, and throughput. We found that DNase treatment of poliovirus RNA followed by random RT, amplification, and the Nextera XT DNA Library Preparation Kit produced significantly better results than other preparations. Average viral reads per total reads, a measurement of efficiency, is as high as 84.2% +/- 15.6%; PV genomes covering >99-100% of the reference length were obtained and validated with Sanger sequencing. A total of 52 PV genomes were generated, multiplexing as many as 64 samples in a single Illumina MiSeq run. This high-throughput, sequence-independent NGS approach can facilitate the detection of a diverse range of PV, especially for those in vaccine-derived polioviruses (VDPV), circulating VDPV, or immunodeficiency-related VDPV. In contrast to previous studies on other viruses, our results showed that filtration and nuclease treatment did not produce discernable increases in sequencing efficiency of PV isolates. However, DNase treatment after nucleic acid extraction to remove host DNA significantly improved sequencing results. This NGS method has been successfully implemented to generate PV genomes for molecular epidemiology of the most recent PV isolates. Additionally, the ability to obtain full PV genomes from FTA cards will aid in facilitating global poliovirus surveillance. |
Reemergence of Dengue in Southern Texas, 2013.
Thomas DL , Santiago GA , Abeyta R , Hinojosa S , Torres-Velasquez B , Adam JK , Evert N , Caraballo E , Hunsperger E , Munoz-Jordan JL , Smith B , Banicki A , Tomashek KM , Gaul L , Sharp TM . Emerg Infect Dis 2016 22 (6) 1002-7 During a dengue epidemic in northern Mexico, enhanced surveillance identified 53 laboratory-positive cases in southern Texas; 26 (49%) patients acquired the infection locally, and 29 (55%) were hospitalized. Of 83 patient specimens that were initially IgM negative according to ELISA performed at a commercial laboratory, 14 (17%) were dengue virus positive by real-time reverse transcription PCR performed at the Centers for Disease Control and Prevention. Dengue virus types 1 and 3 were identified, and molecular phylogenetic analysis demonstrated close identity with viruses that had recently circulated in Mexico and Central America. Of 51 household members of 22 dengue case-patients who participated in household investigations, 6 (12%) had been recently infected with a dengue virus and reported no recent travel, suggesting intrahousehold transmission. One household member reported having a recent illness consistent with dengue. This outbreak reinforces emergence of dengue in southern Texas, particularly when incidence is high in northern Mexico. |
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