Last data update: May 06, 2024. (Total: 46732 publications since 2009)
Records 1-30 (of 74 Records) |
Query Trace: Terry A[original query] |
---|
Reasons for nonparticipation in the Special Supplemental Nutrition Program For Women, Infants, And Children
Terry AL , Wambogo E , Scanlon KS , Fryar CD , Abelev M , Reat A , Ogden CL . JAMA Pediatr 2024 This cross-sectional study evaluates reasons reported for not participating in or withdrawing participation from the Special Supplemental Nutrition Program for Women, Infants, and Children from 2019 to March 2020. | eng |
A diverse group of small circular ssDNA viral genomes in human and non-human primate stools.
Ng TF , Zhang W , Sachsenröder J , Kondov NO , da Costa AC , Vega E , Holtz LR , Wu G , Wang D , Stine CO , Antonio M , Mulvaney US , Muench MO , Deng X , Ambert-Balay K , Pothier P , Vinjé J , Delwart E . Virus Evol 2015 1 (1) vev017 Viral metagenomics sequencing of fecal samples from outbreaks of acute gastroenteritis from the US revealed the presence of small circular ssDNA viral genomes encoding a replication initiator protein (Rep). Viral genomes were ∼2.5 kb in length, with bi-directionally oriented Rep and capsid (Cap) encoding genes and a stem loop structure downstream of Rep. Several genomes showed evidence of recombination. By digital screening of an in-house virome database (1.04 billion reads) using BLAST, we identified closely related sequences from cases of unexplained diarrhea in France. Deep sequencing and PCR detected such genomes in 7 of 25 US (28 percent) and 14 of 21 French outbreaks (67 percent). One of eighty-five sporadic diarrhea cases in the Gambia was positive by PCR. Twenty-two complete genomes were characterized showing that viruses from patients in the same outbreaks were closely related suggesting common origins. Similar genomes were also characterized from the stools of captive chimpanzees, a gorilla, a black howler monkey, and a lemur that were more diverse than the human stool-associated genomes. The name smacovirus is proposed for this monophyletic viral clade. Possible tropism include mammalian enteric cells or ingested food components such as infected plants. No evidence of viral amplification was found in immunodeficient mice orally inoculated with smacovirus-positive stool supernatants. A role for smacoviruses in diarrhea, if any, remains to be demonstrated. |
CDC Grand Rounds: Newborn screening and improved outcomes.
Howell RR , Terry S , Tait VF , Olney R , Hinton CF , Grosse S , Eichwald J , Cuthbert C , Popovic T , Glidewell J . MMWR Morb Mortal Wkly Rep 2012 61 (21) 390-3 Newborn screening is the practice of testing every newborn for certain harmful or potentially fatal conditions, such as hearing loss and certain genetic, endocrine, and metabolic disorders that typically are not otherwise apparent at birth. Newborn screening in the United States began in the 1960s. Universal newborn screening has become a well-established, state-based, public health system involving education, screening, diagnostic follow-up, treatment and management, and system monitoring and evaluation. Each year, >98% of approximately 4 million newborns in the United States are screened. Through early identification, newborn screening provides an opportunity for treatment and significant reductions in morbidity and mortality. |
Improvement in infection prevention and control compliance at the three tertiary hospitals of Sierra Leone following an operational research study
Kamara RZ , Kamara IF , Moses F , Kanu JS , Kallon C , Kabba M , Moffett DB , Fofanah BD , Margao S , Kamara MN , Moiwo MM , Kpagoi Sstk , Tweya HM , Kumar AMV , Terry RF . Trop Med Infect Dis 2023 8 (7) Implementing infection prevention and control (IPC) programmes in line with the World Health Organization's (WHO) eight core components has been challenging in Sierra Leone. In 2021, a baseline study found that IPC compliance in three tertiary hospitals was sub-optimal. We aimed to measure the change in IPC compliance and describe recommended actions at these hospitals in 2023. This was a 'before and after' observational study using two routine cross-sectional assessments of IPC compliance using the WHO IPC Assessment Framework tool. IPC compliance was graded as inadequate (0-200), basic (201-400), intermediate (401-600), and advanced (601-800). The overall compliance scores for each hospital showed an improvement from 'Basic' in 2021 to 'Intermediate' in 2023, with a percentage increase in scores of 16.9%, 18.7%, and 26.9% in these hospitals. There was improved compliance in all core components, with the majority in the 'Intermediate' level for each hospital IPC programme. Recommended actions including the training of healthcare workers and revision of IPC guidelines were undertaken, but a dedicated IPC budget and healthcare-associated infection surveillance remained as gaps in 2023. Operational research is valuable in monitoring and improving IPC programme implementation. To reach the 'Advanced' level, these hospitals should establish a dedicated IPC budget and develop long-term implementation plans. |
The Alaska Native/American Indian experience of hepatitis C treatment with sofosbuvir-based direct-acting antivirals (preprint)
Townshend-Bulson L , Roik E , Barbour Y , Bruden DJT , Homan CE , Espera HGF , Stevenson TJ , Hewitt AM , Rhodes W , Gove JE , Plotnik JN , Snowball MM , McGilvray J , Simons BC , McMahon BJ . medRxiv 2021 2021.09.03.21263089 Background Direct-acting antiviral (DAA) drugs have been effective in the treatment of chronic hepatitis C virus (HCV) infection. Limited data are available on safety, tolerability, and efficacy in American Indian or Alaska Native people. We aim to evaluate the treatment outcomes of sofosbuvir-based regimens for treatment of HCV in a real life setting in Alaska Native/American Indian (AN/AI) people.Methods AN/AI patients within the Alaska Tribal Health System with confirmed positive anti-HCV and HCV RNA, who were 18 years of age and older were included in the study. Pretreatment baseline patient characteristics, treatment efficacy based on sustained virologic response (SVR) 12 weeks after treatment completion, and adverse effects were assessed. The following treatments were given according to the American Association for the Study of Liver Diseases/Infectious Disease Society of America (AASLD/IDSA) HCV Guidance: ledipasvir/sofosbuvir, sofosbuvir plus weight-based ribavirin, and sofosbuvir/velpatasvir.Results We included 501 patients with a mean age of 54.3 (range 21.3 -78.3) in the study. Overall SVR was achieved in 95.2% of patients who received one of the three DAA regimens. For those with cirrhosis, overall SVR was 92.8% and for those with genotype 3 91.1% achieved SVR. The most common symptom experienced during treatment was headache. Joint pain was found to decrease during treatment. One person discontinued sofosbuvir plus ribavirin due to myocardial infarction and one discontinued sofosbuvir/velpatasvir due to urticaria.Conclusions In the real-world setting, sofosbuvir-based treatment is safe, effective, and well tolerated in AN/AI patients. Sustained virologic response was high regardless of HCV genotype or cirrhosis status.Competing Interest StatementPartial funding from Gilead Sciences.Funding StatementPartial funding from Gilead Sciences.Author DeclarationsI confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.YesThe details of the IRB/oversight body that provided approval or exemption for the research described are given below:Alaska Area Institutional Review Board (IHS IRB #2) Dr. Shanda Lohse, Chair, Alaska Area IRB Terry Powell, Administrator, Alaska Area IRB 4315 Diplomacy Drive - RMCC Anchorage, AK 99508 Phone: 907-729-3924 or 907-729-3917 Email: akaalaskaareaIRB{at}anthc.orgAll necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).YesI have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable.YesAccess to data for this study is subject to tribal review. Requests for data should be directed to the Alaska Native Tribal Health Consortium Privacy Officer c/o Ethics and Compliance Services, 4315 Diplomacy Drive, Anchorage, AK 99508. |
Dairy, meat, seafood, and plant sources of saturated fat: United States, ages 2 years and over, 2017-2020
Wambogo EA , Ansai N , Terry A , Fryar C , Ogden C . J Nutr 2023 153 (9) 2689-2698 BACKGROUND: Research suggests that the effects of saturated fat (SF) on health differ depending on its food source. Dairy SF has been associated with lower cardiovascular disease (CVD) risk, while meat SF is linked to a higher CVD risk. OBJECTIVES: To estimate the contribution to total intake of SF of, (1) 5 food groups - dairy, meats, seafood, plants, and "other", and (2) the top 10 specific food category sources in the US population overall and by sociodemographic subgroup. METHODS: Analysis included data from 11,798 participants in the 2017-March 2020 NHANES aged 2+ years. Grams of SF from the food sources, expressed as a percentage of the total grams of SF consumed, were estimated using the population ratio method. RESULTS: Mean daily intake of SF was 28.1g (95% CI: 27.6-28.6g), comprising 11.9% (95% CI: 11.7-12.1%) of total energy intake. Dairy contributed 28.4% of SF, followed by meats (22.1%), plant sources (7.5%), fish and seafood (1.2%), and the remaining foods (41.6%). Youth had higher SF intake from dairy than adults (p<0.001), while non-Hispanic Whites had higher intake than non-Hispanic Blacks (NHB) (p<0.001) and Hispanics (p=0.016). Adults had higher SF intake from meats than youth (p=0.002), males more than females (p<0.001), and NHB more than non-Hispanic Asians (P=0.016) and Hispanics (P<0.001). The top 10 specific sources of SF were unprocessed red meats, sweet bakery products, cured meats, milk, cheese, pizza, unprocessed poultry, Mexican mixed dishes, eggs, and combined fruits and vegetables. CONCLUSIONS: Although dairy contributed about 30% of SF compared to about 20% for total meat, the top specific food category source of SF was unprocessed red meats, which ranked in the top 2 food category sources of SF for most subgroups. These findings may be useful for further research to examine the relationship between the different sources of SF and health outcomes. |
A Public Health Research Agenda for Managing Infodemics: Methods and Results of the First WHO Infodemiology Conference.
Calleja N , AbdAllah A , Abad N , Ahmed N , Albarracin D , Altieri E , Anoko JN , Arcos R , Azlan AA , Bayer J , Bechmann A , Bezbaruah S , Briand SC , Brooks I , Bucci LM , Burzo S , Czerniak C , De Domenico M , Dunn AG , Ecker UKH , Espinosa L , Francois C , Gradon K , Gruzd A , Gülgün BS , Haydarov R , Hurley C , Astuti SI , Ishizumi A , Johnson N , Johnson Restrepo D , Kajimoto M , Koyuncu A , Kulkarni S , Lamichhane J , Lewis R , Mahajan A , Mandil A , McAweeney E , Messer M , Moy W , Ndumbi Ngamala P , Nguyen T , Nunn M , Omer SB , Pagliari C , Patel P , Phuong L , Prybylski D , Rashidian A , Rempel E , Rubinelli S , Sacco P , Schneider A , Shu K , Smith M , Sufehmi H , Tangcharoensathien V , Terry R , Thacker N , Trewinnard T , Turner S , Tworek H , Uakkas S , Vraga E , Wardle C , Wasserman H , Wilhelm E , Würz A , Yau B , Zhou L , Purnat TD . JMIR Infodemiology 2021 1 (1) e30979 BACKGROUND: An infodemic is an overflow of information of varying quality that surges across digital and physical environments during an acute public health event. It leads to confusion, risk-taking, and behaviors that can harm health and lead to erosion of trust in health authorities and public health responses. Owing to the global scale and high stakes of the health emergency, responding to the infodemic related to the pandemic is particularly urgent. Building on diverse research disciplines and expanding the discipline of infodemiology, more evidence-based interventions are needed to design infodemic management interventions and tools and implement them by health emergency responders. OBJECTIVE: The World Health Organization organized the first global infodemiology conference, entirely online, during June and July 2020, with a follow-up process from August to October 2020, to review current multidisciplinary evidence, interventions, and practices that can be applied to the COVID-19 infodemic response. This resulted in the creation of a public health research agenda for managing infodemics. METHODS: As part of the conference, a structured expert judgment synthesis method was used to formulate a public health research agenda. A total of 110 participants represented diverse scientific disciplines from over 35 countries and global public health implementing partners. The conference used a laddered discussion sprint methodology by rotating participant teams, and a managed follow-up process was used to assemble a research agenda based on the discussion and structured expert feedback. This resulted in a five-workstream frame of the research agenda for infodemic management and 166 suggested research questions. The participants then ranked the questions for feasibility and expected public health impact. The expert consensus was summarized in a public health research agenda that included a list of priority research questions. RESULTS: The public health research agenda for infodemic management has five workstreams: (1) measuring and continuously monitoring the impact of infodemics during health emergencies; (2) detecting signals and understanding the spread and risk of infodemics; (3) responding and deploying interventions that mitigate and protect against infodemics and their harmful effects; (4) evaluating infodemic interventions and strengthening the resilience of individuals and communities to infodemics; and (5) promoting the development, adaptation, and application of interventions and toolkits for infodemic management. Each workstream identifies research questions and highlights 49 high priority research questions. CONCLUSIONS: Public health authorities need to develop, validate, implement, and adapt tools and interventions for managing infodemics in acute public health events in ways that are appropriate for their countries and contexts. Infodemiology provides a scientific foundation to make this possible. This research agenda proposes a structured framework for targeted investment for the scientific community, policy makers, implementing organizations, and other stakeholders to consider. |
Trends in food consumption among children aged 1-4 years by participation in the Special Supplemental Nutrition Program for Women, Infants, and Children, United States, 2005-2018
Fryar CD , Wambogo EA , Scanlon KS , Terry AL , Ogden CL . J Nutr 2023 153 (3) 839-847 BACKGROUND: In 2009, the US Department of Agriculture Food and Nutrition Service's Special Supplemental Nutrition Program for Women, Infants, and Children (WIC) food packages were revised to include more whole fruits, vegetables, whole grains, and lower-fat milk. OBJECTIVE: To describe trends over time in the consumption of fruits (total and whole), vegetables, whole grains, milk (whole, reduced fat, low-fat or nonfat (LFNF), and flavored), and added sugars, including breakfast cereals, by WIC participation status (current WIC recipient, WIC income-eligible nonrecipient, and WIC income-ineligible nonrecipient). METHODS: Dietary intakes on a given day for 1- to 4-y-old children (n = 5568) from the 2005-2018 National Health and Nutrition Examination Survey (NHANES) were analyzed to examine trends in the percentage of individuals consuming and amounts consumed over time using linear regression adjusted for age, sex, and race and Hispanic origin. RESULTS: From 2005 through 2018, the percentage of WIC recipients or WIC income-eligible nonrecipients consuming fruits and vegetables on a given day did not change, but the percentage of fruit consumed as whole fruit increased significantly among WIC recipients (36.4%-62.1%), but not among income-eligible nonrecipients. Among the WIC recipients, the percentage of consumption (5.5%-29.3%), the amount of LFNF milk servings consumed (0.1-0.4 cups), and the percentage of the total milk consumed as LFNF milk (4.8%-27%) significantly increased from 2005 to 2018. Conversely, the percentage of energy (12.3%-10.8%) and servings (11.4-10.6 teaspoons) from added sugars declined significantly. Among WIC-eligible nonrecipients, the servings of whole grains increased significantly, whereas servings and percentage of energy from added sugars declined significantly. CONCLUSIONS: From 2005 through 2018, changes in dietary patterns for WIC recipients did not always mirror those of US children of the same age. The percentage of fruit consumed as whole fruit, and the percentage and quantity of milk consumed as LFNF milk increased significantly among WIC recipients, but not among income-eligible nonrecipients. J Nutr 20XX;xx:xx-xx. |
Prospective cohort study of children with suspected SARS-CoV-2 infection presenting to paediatric emergency departments: a Paediatric Emergency Research Networks (PERN) Study Protocol.
Funk AL , Florin TA , Dalziel SR , Mintegi S , Salvadori MI , Tancredi DJ , Neuman MI , Payne DC , Plint AC , Klassen TP , Malley R , Ambroggio L , Kim K , Kuppermann N , Freedman SB . BMJ Open 2021 11 (1) e042121 INTRODUCTION: Relatively limited data are available regarding paediatric COVID-19. Although most children appear to have mild or asymptomatic infections, infants and those with comorbidities are at increased risk of experiencing more severe illness and requiring hospitalisation due to COVID-19. The recent but uncommon association of SARS-CoV-2 infection with development of a multisystem inflammatory syndrome has heightened the importance of understanding paediatric SARS-CoV-2 infection. METHODS AND ANALYSIS: The Paediatric Emergency Research Network-COVID-19 cohort study is a rapid, global, prospective cohort study enrolling 12 500 children who are tested for acute SARS-CoV-2 infection. 47 emergency departments across 12 countries on four continents will participate. At enrolment, regardless of SARS-CoV-2 test results, all children will have the same information collected, including clinical, epidemiological, laboratory, imaging and outcome data. Interventions and outcome data will be collected for hospitalised children. For all children, follow-up at 14 and 90 days will collect information on further medical care received, and long-term sequelae, respectively. Statistical models will be designed to identify risk factors for infection and severe outcomes. ETHICS AND DISSEMINATION: Sites will seek ethical approval locally, and informed consent will be obtained. There is no direct risk or benefit of study participation. Weekly interim analysis will allow for real-time data sharing with regional, national, and international policy makers. Harmonisation and sharing of investigation materials with WHO, will contribute to synergising global efforts for the clinical characterisation of paediatric COVID-19. Our findings will enable the implementation of countermeasures to reduce viral transmission and severe COVID-19 outcomes in children. TRIAL REGISTRATION NUMBER: NCT04330261. |
Metagenomic sequencing generates the whole genomes of porcine rotavirus A, C, and H from the United States.
Hull JJA , Qi M , Montmayeur AM , Kumar D , Velasquez DE , Moon SS , Magaña LC , Betrapally N , Ng TFF , Jiang B , Marthaler D . PLoS One 2020 15 (12) e0244498 The genus Rotavirus comprises eight species, designated A to H, and two recently identified tentative species I in dogs and J in bats. Species Rotavirus A, B, C and H (RVA, RVB, RVC and RVH) have been detected in humans and animals. While human and animal RVA are well characterized and defined, complete porcine genome sequences in the GenBank are limited compared to human strains. Here, we used a metagenomic approach to sequence the 11 segments of RVA, RVC and RVH strains from piglets in the United States (US) and explore the evolutionary relations of these RV species. Metagenomics identified Astroviridae, Picornaviridae, Caliciviridae, Coronoviridae in samples MN9.65 and OK5.68 while Picobirnaviridae and Arteriviridae were only identified in sample OK5.68. Whole genome sequencing and phylogenetic analyses identified multiple genotypes with the RVA of strain MN9.65 and OK5.68, with the genome constellation of G5/G9-P[7]/P[13]-I5/I5- R1/R1-C1-M1-A8-N1-T7-E1/E1-H1 and G5/G9-P[6]/P[7]-I5-R1/R1-C1-M1-A8-N1-T1/T7-E1/E1-H1, respectively. The RVA strains had a complex evolutionary relationship with other mammalian strains. The RVC strain OK5.68 had a genome constellation of G9-P[6]-I1-R1-C5-M6-A5-N1-T1-E1-H1, and shared an evolutionary relationship with porcine strains from the US. The RVH strains MN9.65 and OK5.68 had the genome constellation of G5-P1-I1-R1-C1-M1-A5-N1-T1-E4-H1 and G5-P1-I1-R1-C1-M1-A5-N1-T1-E1-H1, indicating multiple RVH genome constellations are circulating in the US. These findings allow us to understand the complexity of the enteric virome, develop improved screening methods for RVC and RVH strains, facilitate expanded rotavirus surveillance in pigs, and increase our understanding of the origin and evolution of rotavirus species. |
Framework for a Community Health Observing System for the Gulf of Mexico Region: Preparing for Future Disasters.
Sandifer P , Knapp L , Lichtveld M , Manley R , Abramson D , Caffey R , Cochran D , Collier T , Ebi K , Engel L , Farrington J , Finucane M , Hale C , Halpern D , Harville E , Hart L , Hswen Y , Kirkpatrick B , McEwen B , Morris G , Orbach R , Palinkas L , Partyka M , Porter D , Prather AA , Rowles T , Scott G , Seeman T , Solo-Gabriele H , Svendsen E , Tincher T , Trtanj J , Walker AH , Yehuda R , Yip F , Yoskowitz D , Singer B . Front Public Health 2020 8 578463 The Gulf of Mexico (GoM) region is prone to disasters, including recurrent oil spills, hurricanes, floods, industrial accidents, harmful algal blooms, and the current COVID-19 pandemic. The GoM and other regions of the U.S. lack sufficient baseline health information to identify, attribute, mitigate, and facilitate prevention of major health effects of disasters. Developing capacity to assess adverse human health consequences of future disasters requires establishment of a comprehensive, sustained community health observing system, similar to the extensive and well-established environmental observing systems. We propose a system that combines six levels of health data domains, beginning with three existing, national surveys and studies plus three new nested, longitudinal cohort studies. The latter are the unique and most important parts of the system and are focused on the coastal regions of the five GoM States. A statistically representative sample of participants is proposed for the new cohort studies, stratified to ensure proportional inclusion of urban and rural populations and with additional recruitment as necessary to enroll participants from particularly vulnerable or under-represented groups. Secondary data sources such as syndromic surveillance systems, electronic health records, national community surveys, environmental exposure databases, social media, and remote sensing will inform and augment the collection of primary data. Primary data sources will include participant-provided information via questionnaires, clinical measures of mental and physical health, acquisition of biological specimens, and wearable health monitoring devices. A suite of biomarkers may be derived from biological specimens for use in health assessments, including calculation of allostatic load, a measure of cumulative stress. The framework also addresses data management and sharing, participant retention, and system governance. The observing system is designed to continue indefinitely to ensure that essential pre-, during-, and post-disaster health data are collected and maintained. It could also provide a model/vehicle for effective health observation related to infectious disease pandemics such as COVID-19. To our knowledge, there is no comprehensive, disaster-focused health observing system such as the one proposed here currently in existence or planned elsewhere. Significant strengths of the GoM Community Health Observing System (CHOS) are its longitudinal cohorts and ability to adapt rapidly as needs arise and new technologies develop. |
Top food category contributors to sodium and potassium intake - United States, 2015-2016
Woodruff RC , Zhao L , Ahuja JKC , Gillespie C , Goldman J , Harris DM , Jackson SL , Moshfegh A , Rhodes D , Sebastian RS , Terry A , Cogswell ME . MMWR Morb Mortal Wkly Rep 2020 69 (32) 1064-1069 Most U.S. adults consume too much sodium and not enough potassium (1,2). For apparently healthy U.S. adults aged ≥19 years, guidelines recommend reducing sodium intake that exceeds 2,300 mg/day and consuming at least 3,400 mg/day of potassium for males and at least 2,600 mg/day for females* (1). Reducing population-level sodium intake can reduce blood pressure and prevent cardiovascular diseases, the leading causes of death in the United States (1,3). Adequate potassium intake might offset the hypertensive effects of excessive sodium intake (1). Data from the 2015-2016 What We Eat in America (WWEIA) dietary interview component of the National Health and Nutrition Examination Survey (NHANES)(†) were analyzed to identify top food categories contributing to sodium and potassium intake for U.S. residents aged ≥1 year. During 2015-2016, 40% of sodium consumed came from the top 10 food categories, which included prepared foods with sodium added (e.g., deli meat sandwiches and pizza). Approximately 43% of potassium consumed was from 10 food categories, which included foods naturally low in sodium (e.g., unflavored milk, fruit, vegetables) and prepared foods. These results can inform efforts to encourage consumption of foods naturally low in sodium, which might have the dual benefit of reducing sodium intake and increasing potassium intake, contributing to cardiovascular disease prevention. |
The effect of variant interference on de novo assembly for viral deep sequencing.
Castro CJ , Marine RL , Ramos E , Ng TFF . BMC Genomics 2020 21 (1) 421 BACKGROUND: Viruses have high mutation rates and generally exist as a mixture of variants in biological samples. Next-generation sequencing (NGS) approaches have surpassed Sanger for generating long viral sequences, yet how variants affect NGS de novo assembly remains largely unexplored. RESULTS: Our results from > 15,000 simulated experiments showed that presence of variants can turn an assembly of one genome into tens to thousands of contigs. This "variant interference" (VI) is highly consistent and reproducible by ten commonly-used de novo assemblers, and occurs over a range of genome length, read length, and GC content. The main driver of VI is pairwise identities between viral variants. These findings were further supported by in silico simulations, where selective removal of minor variant reads from clinical datasets allow the "rescue" of full viral genomes from fragmented contigs. CONCLUSIONS: These results call for careful interpretation of contigs and contig numbers from de novo assembly in viral deep sequencing. |
Human monkeypox - After 40 years, an unintended consequence of smallpox eradication.
Simpson K , Heymann D , Brown CS , Edmunds WJ , Elsgaard J , Fine P , Hochrein H , Hoff NA , Green A , Ihekweazu C , Jones TC , Lule S , Maclennan J , McCollum A , Muhlemann B , Nightingale E , Ogoina D , Ogunleye A , Petersen B , Powell J , Quantick O , Rimoin AW , Ulaeato D , Wapling A . Vaccine 2020 38 (33) 5077-5081 Smallpox eradication, coordinated by the WHO and certified 40 years ago, led to the cessation of routine smallpox vaccination in most countries. It is estimated that over 70% of the world's population is no longer protected against smallpox, and through cross-immunity, to closely related orthopox viruses such as monkeypox. Monkeypox is now a re-emerging disease. Monkeypox is endemic in as yet unconfirmed animal reservoirs in sub-Saharan Africa, while its human epidemiology appears to be changing. Monkeypox in small animals imported from Ghana as exotic pets was at the origin of an outbreak of human monkeypox in the USA in 2003. Travellers infected in Nigeria were at the origin of monkeypox cases in the UK in 2018 and 2019, Israel in 2018 and Singapore in2019. Together with sporadic reports of human infections with other orthopox viruses, these facts invite speculation that emergent or re-emergent human monkeypox might fill the epidemiological niche vacated by smallpox. An ad-hoc and unofficial group of interested experts met to consider these issues at Chatham House, London in June 2019, in order to review available data and identify monkeypox-related research gaps. Gaps identified by the experts included:The experts further agreed on the need for a better understanding of the genomic evolution and changing epidemiology of orthopox viruses, the usefulness of in-field genomic diagnostics, and the best disease control strategies, including the possibility of vaccination with new generation non-replicating smallpox vaccines and treatment with recently developed antivirals. |
Analysis of the reiteration regions (R1 to R5) of varicella-zoster virus.
Jensen NJ , Depledge DP , Ng TFF , Leung J , Quinlivan M , Radford KW , Folster J , Tseng HF , LaRussa P , Jacobsen SJ , Breuer J , Schmid DS . Virology 2020 546 38-50 The varicella-zoster virus (VZV) genome, comprises both unique and repeated regions. The genome also includes reiteration regions, designated R1 to R5, which are tandemly repeating sequences termed elements. These regions represent an understudied feature of the VZV genome. The R4 region is duplicated, with one copy in the internal repeat short (IRs) which we designated R4A and a second copy in the terminal repeat short (TRs) termed R4B. We developed primers to amplify and Sanger sequence these regions, including independent amplification of both R4 regions. Reiteration regions from >80 cases of PCR-confirmed shingles were sequenced and analyzed. Complete genome sequences for the remaining portions of these viruses were determined using Illumina MiSeq. We identified 28 elements not previously reported, including at least one element for each R region. Length heterogeneity was substantial in R3, R4A and R4B. Length heterogeneity between the two copies of R4 was common. |
Comparison of Illumina MiSeq and the Ion Torrent PGM and S5 platforms for whole-genome sequencing of picornaviruses and caliciviruses.
Marine RL , Magana LC , Castro CJ , Zhao K , Montmayeur AM , Schmidt A , Diez-Valcarce M , Fan Ng TF , Vinje J , Burns CC , Allan Nix W , Rota PA , Oberste MS . J Virol Methods 2020 280 113865 Next-generation sequencing is a powerful tool for virological surveillance. While Illumina(R) and Ion Torrent(R) sequencing platforms are used extensively for generating viral RNA genome sequences, there is limited data comparing different platforms. The Illumina MiSeq, Ion Torrent PGM and Ion Torrent S5 platforms were evaluated using a panel of sixteen specimens containing picornaviruses and human caliciviruses (noroviruses and sapoviruses). The specimens were processed, using combinations of three library preparation and five sequencing kits, to assess the quality and completeness of assembled viral genomes, and an estimation of cost per sample to generate the data was calculated. The choice of library preparation kit and sequencing platform was found to impact the breadth of genome coverage and accuracy of consensus viral genomes. The Ion Torrent S5 510 chip runs produced more reads at a lower cost per sample than the highest output Ion Torrent PGM 318 chip run, and generated the highest proportion of reads for enterovirus D68 samples. However, indels at homopolymer regions impacted the accuracy of consensus genome sequences. For lower throughput sequencing runs (i.e., Ion Torrent 510 and Illumina MiSeq Nano V2), the cost per sample was lower on the MiSeq platform, whereas with higher throughput runs (Ion Torrent 530 and Illumina MiSeq V2) there is less of a difference in the cost per sample between the two sequencing platforms ($5.47-$10.25 more per sample for an Ion Torrent 530 chip run when multiplexing 24 samples). These findings suggest that the Ion Torrent S5 and Illumina MiSeq platforms are both viable options for genomic sequencing of RNA viruses, each with specific advantages and tradeoffs. |
Antifungal triazole posaconazole targets an early stage of the parechovirus A3 life cycle.
Rhoden E , Ng TFF , Campagnoli R , Nix WA , Konopka-Anstadt J , Selvarangan R , Briesach L , Oberste MS , Weldon WC . Antimicrob Agents Chemother 2019 64 (3) Viruses in species Parechovirus A (Picornaviridae) are associated with a wide variety of clinical manifestations. Parechovirus A3 (PeV-A3) is known to cause sepsis-like illness, meningitis, and encephalitis in infants and young children. To date, no specific therapies are available to treat PeV-A3-infected children. We had previously identified two FDA-cleared antifungal drugs, itraconazole (ITC) and posaconazole (POS) with potent and specific antiviral activity against PeV-A3. Time-of-addition and synchronized infection assays revealed that POS targets an early stage of the PeV-A3 life cycle. POS exerts an antiviral effect, evidenced by a reduction in viral titer following the addition of POS to Vero-P cells before infection, coaddition of POS and PeV-A3 to Vero-P cells, incubation of POS and PeV-A3 prior to Vero-P infection, and at attachment. POS exerts less of an effect on virus entry. A PeV-A3 ELISA inhibition experiment, using an anti-PeV-A3 monoclonal antibody (mAb), suggested that POS binds directly to the PeV-A3 capsid. POS-resistant PeV-A3 strains developed by serial passage in the presence of POS, acquired substitutions in multiple regions of the genome, including the capsid. Reverse genetics confirmed substitutions in capsid proteins VP0, VP3, VP1 and nonstructural proteins 2A and 3A. Single mutants VP0_K66R, VP0_A124T, VP3_N88S, VP1_Y224C, 2A_S788L and 3A_T1I were respectively 4-, 9-, 12-, 34-, 51-, and 119-fold more resistant to POS than its susceptible prototype strain. Our studies demonstrate that POS may be a valuable tool in developing an antiviral therapy for PeV-A3. |
An open challenge to advance probabilistic forecasting for dengue epidemics.
Johansson MA , Apfeldorf KM , Dobson S , Devita J , Buczak AL , Baugher B , Moniz LJ , Bagley T , Babin SM , Guven E , Yamana TK , Shaman J , Moschou T , Lothian N , Lane A , Osborne G , Jiang G , Brooks LC , Farrow DC , Hyun S , Tibshirani RJ , Rosenfeld R , Lessler J , Reich NG , Cummings DAT , Lauer SA , Moore SM , Clapham HE , Lowe R , Bailey TC , Garcia-Diez M , Carvalho MS , Rodo X , Sardar T , Paul R , Ray EL , Sakrejda K , Brown AC , Meng X , Osoba O , Vardavas R , Manheim D , Moore M , Rao DM , Porco TC , Ackley S , Liu F , Worden L , Convertino M , Liu Y , Reddy A , Ortiz E , Rivero J , Brito H , Juarrero A , Johnson LR , Gramacy RB , Cohen JM , Mordecai EA , Murdock CC , Rohr JR , Ryan SJ , Stewart-Ibarra AM , Weikel DP , Jutla A , Khan R , Poultney M , Colwell RR , Rivera-Garcia B , Barker CM , Bell JE , Biggerstaff M , Swerdlow D , Mier YTeran-Romero L , Forshey BM , Trtanj J , Asher J , Clay M , Margolis HS , Hebbeler AM , George D , Chretien JP . Proc Natl Acad Sci U S A 2019 116 (48) 24268-24274 A wide range of research has promised new tools for forecasting infectious disease dynamics, but little of that research is currently being applied in practice, because tools do not address key public health needs, do not produce probabilistic forecasts, have not been evaluated on external data, or do not provide sufficient forecast skill to be useful. We developed an open collaborative forecasting challenge to assess probabilistic forecasts for seasonal epidemics of dengue, a major global public health problem. Sixteen teams used a variety of methods and data to generate forecasts for 3 epidemiological targets (peak incidence, the week of the peak, and total incidence) over 8 dengue seasons in Iquitos, Peru and San Juan, Puerto Rico. Forecast skill was highly variable across teams and targets. While numerous forecasts showed high skill for midseason situational awareness, early season skill was low, and skill was generally lowest for high incidence seasons, those for which forecasts would be most valuable. A comparison of modeling approaches revealed that average forecast skill was lower for models including biologically meaningful data and mechanisms and that both multimodel and multiteam ensemble forecasts consistently outperformed individual model forecasts. Leveraging these insights, data, and the forecasting framework will be critical to improve forecast skill and the application of forecasts in real time for epidemic preparedness and response. Moreover, key components of this project-integration with public health needs, a common forecasting framework, shared and standardized data, and open participation-can help advance infectious disease forecasting beyond dengue. |
Nearly Complete Genome Sequence of an Echovirus 30 Strain from a Cluster of Aseptic Meningitis Cases in California, September 2017.
Pan CY , Huynh T , Padilla T , Chen A , Ng TFF , Marine RL , Castro CJ , Nix WA , Wadford DA . Microbiol Resour Announc 2019 8 (44) We report the nearly complete genome sequence of a human enterovirus, a strain of echovirus 30, obtained from a cerebrospinal fluid specimen from a teenaged patient with aseptic meningitis in September 2017. |
Pan-viral serology implicates enteroviruses in acute flaccid myelitis.
Schubert RD , Hawes IA , Ramachandran PS , Ramesh A , Crawford ED , Pak JE , Wu W , Cheung CK , O'Donovan BD , Tato CM , Lyden A , Tan M , Sit R , Sowa GA , Sample HA , Zorn KC , Banerji D , Khan LM , Bove R , Hauser SL , Gelfand AA , Johnson-Kerner BL , Nash K , Krishnamoorthy KS , Chitnis T , Ding JZ , McMillan HJ , Chiu CY , Briggs B , Glaser CA , Yen C , Chu V , Wadford DA , Dominguez SR , Ng TFF , Marine RL , Lopez AS , Nix WA , Soldatos A , Gorman MP , Benson L , Messacar K , Konopka-Anstadt JL , Oberste MS , DeRisi JL , Wilson MR . Nat Med 2019 25 (11) 1748-1752 Since 2012, the United States of America has experienced a biennial spike in pediatric acute flaccid myelitis (AFM)(1-6). Epidemiologic evidence suggests non-polio enteroviruses (EVs) are a potential etiology, yet EV RNA is rarely detected in cerebrospinal fluid (CSF)(2). CSF from children with AFM (n = 42) and other pediatric neurologic disease controls (n = 58) were investigated for intrathecal antiviral antibodies, using a phage display library expressing 481,966 overlapping peptides derived from all known vertebrate and arboviruses (VirScan). Metagenomic next-generation sequencing (mNGS) of AFM CSF RNA (n = 20 cases) was also performed, both unbiased sequencing and with targeted enrichment for EVs. Using VirScan, the viral family significantly enriched by the CSF of AFM cases relative to controls was Picornaviridae, with the most enriched Picornaviridae peptides belonging to the genus Enterovirus (n = 29/42 cases versus 4/58 controls). EV VP1 ELISA confirmed this finding (n = 22/26 cases versus 7/50 controls). mNGS did not detect additional EV RNA. Despite rare detection of EV RNA, pan-viral serology frequently identified high levels of CSF EV-specific antibodies in AFM compared with controls, providing further evidence for a causal role of non-polio EVs in AFM. |
Outbreak of diarrhoea in piglets caused by novel rotavirus genotype G4P[49] in north-western district of Bangladesh, February 2014.
Sarkar S , Dioh Esona M , Gautam R , Castro CJ , Ng TFF , Haque W , Khan SU , Hossain ME , Rahman MZ , Gurley ES , Kennedy ED , Bowen MD , Parashar UD , Rahman M . Transbound Emerg Dis 2019 67 (1) 442-449 Group A rotavirus (RVA) associated diarrhea in piglets represents one of the major causes of morbidity and mortality in pig farms worldwide. A diarrhea outbreak occurred among nomadic piglets in north-western district of Bangladesh in February 2014. Outbreak investigation was performed to identify the cause, epidemiologic and clinical features of the outbreak. Rectal swabs and clinical information were collected from diarrheic piglets (n=36). Rectal swabs were tested for RVA RNA by real time reverse transcription polymerase chain reaction (rRT-PCR) using NSP3-specific primers. The G (VP7) and P (VP4) genes were typed by conventional RT-PCR and sanger sequencing and full genome sequences were determined using next generation sequencing. We found the attack rate was 61% (50/82) among piglets in the nomadic pig herd and the case fatality rate was 20% (10/50) among piglets with diarrhea. All study piglets cases had watery diarrhea, lack of appetite or reluctance to move. A novel RVA strain with a new P[49] genotype combined with G4 was identified among all piglets with diarrhea. The genome constellation of the novel RVA strains was determined to be G4-P [49]-I1-R1-C1-M1-A8-N1-T7-E1-H1. Genetic analysis shows that the novel G4P[49] strain is similar to Indian and Chinese porcine or porcine-like G4 human strains and is genetically distant from Bangladeshi human G4 strains. Identification of this novel RVA strain warrants further exploration for disease severity and zoonotic potential. This article is protected by copyright. All rights reserved. |
Antibodies to Enteroviruses in Cerebrospinal Fluid of Patients with Acute Flaccid Myelitis.
Mishra N , Ng TFF , Marine RL , Jain K , Ng J , Thakkar R , Caciula A , Price A , Garcia JA , Burns JC , Thakur KT , Hetzler KL , Routh JA , Konopka-Anstadt JL , Nix WA , Tokarz R , Briese T , Oberste MS , Lipkin WI . mBio 2019 10 (4) Acute flaccid myelitis (AFM) has caused motor paralysis in >560 children in the United States since 2014. The temporal association of enterovirus (EV) outbreaks with increases in AFM cases and reports of fever, respiratory, or gastrointestinal illness prior to AFM in >90% of cases suggest a role for infectious agents. Cerebrospinal fluid (CSF) from 14 AFM and 5 non-AFM patients with central nervous system (CNS) diseases in 2018 were investigated by viral-capture high-throughput sequencing (VirCapSeq-VERT system). These CSF and serum samples, as well as multiple controls, were tested for antibodies to human EVs using peptide microarrays. EV RNA was confirmed in CSF from only 1 adult AFM case and 1 non-AFM case. In contrast, antibodies to EV peptides were present in CSF of 11 of 14 AFM patients (79%), significantly higher than controls, including non-AFM patients (1/5 [20%]), children with Kawasaki disease (0/10), and adults with non-AFM CNS diseases (2/11 [18%]) (P = 0.023, 0.0001, and 0.0028, respectively). Six of 14 CSF samples (43%) and 8 of 11 sera (73%) from AFM patients were immunoreactive to an EV-D68-specific peptide, whereas the three control groups were not immunoreactive in either CSF (0/5, 0/10, and 0/11; P = 0.008, 0.0003, and 0.035, respectively) or sera (0/2, 0/8, and 0/5; P = 0.139, 0.002, and 0.009, respectively).IMPORTANCE The presence in cerebrospinal fluid of antibodies to EV peptides at higher levels than non-AFM controls supports the plausibility of a link between EV infection and AFM that warrants further investigation and has the potential to lead to strategies for diagnosis and prevention of disease. |
Get in, get tested, get care: STD services in urban urgent care centers
Williams SP , Kinsey J , Carry MG , Terry L , Wells J , Kroeger K . Sex Transm Dis 2019 46 (10) 648-653 BACKGROUND: Recent evidence indicates increased use of urgent care centers (UCCs) for STD testing. We sought to learn more about STD services in UCCs in a large metropolitan area. METHOD: Using a modified rapid gap assessment approach, we interviewed staff from 19 UCCs in metro Atlanta, GA USA. The UCCs were identified using two online search engines. We focused on a 50-mile radius around Atlanta. We then excluded duplicates and closed UCCs, and ones outside Atlanta's five contiguous counties. Using a prioritization process, we visited UCCs in or adjacent to areas with mid-high local STD morbidity, or facilities from which STD cases were reported the year prior. We collected checklist-based data on STD testing, treatment and preventive services, as well as supportive services (e.g., substance use/mental health referrals). Checklist data, notes, and open-ended questions were summarized and analyzed descriptively. RESULTS: All UCCs (n=19) reported offering basic to comprehensive STD testing. Although most could treat on-site for chlamydia and gonorrhea, most relied on referrals, or prescriptions and "return to facility" practices to treat syphilis. Sources for STD information/management included the HD/CDC, online medical sites, and EMR embedded information. Challenges UCCs acknowledged included staying up-to-date with treatment guidance and lab reporting requirements, inadequate time for sexual risk reduction counseling, and linking patients with extended care needs (e.g., HIV+ case management, supportive services), or following up with patients. CONCLUSIONS: Urgent cares are STD testing resources. Service availability varies, but opportunities exists to enhance STD services in UCC settings and in communities. |
Evaluation of measurement error in 24-hour dietary recall for assessing sodium and potassium intake among US adults - National Health and Nutrition Examination Survey (NHANES), 2014
Va P , Dodd KW , Zhao L , Thompson-Paul AM , Mercado CI , Terry AL , Jackson SL , Wang CY , Loria CM , Moshfegh AJ , Rhodes DG , Cogswell ME . Am J Clin Nutr 2019 109 (6) 1672-1682 BACKGROUND: Understanding measurement error in sodium and potassium intake is essential for assessing population intake and studying associations with health outcomes. OBJECTIVE: The aim of this study was to compare sodium and potassium intake derived from 24-h dietary recall (24HDR) with intake derived from 24-h urinary excretion (24HUE). DESIGN: Data were analyzed from 776 nonpregnant, noninstitutionalized US adults aged 20-69 y who completed 1-to-2 24HUE and 24HDR measures in the 2014 NHANES. A total of 1190 urine specimens and 1414 dietary recalls were analyzed. Mean bias was estimated as mean of the differences between individual mean 24HDR and 24HUE measurements. Correlations and attenuation factors were estimated using the Kipnis joint-mixed effects model accounting for within-person day-to-day variability in sodium excretion. The attenuation factor reflects the degree to which true associations between long-term intake (estimated using 24HUEs) and a hypothetical health outcome would be approximated using a single 24HDR: values near 1 indicate close approximation and near 0 indicate bias toward null. Estimates are reported for sodium, potassium, and the sodium: potassium (Na/K) ratio. Model parameters can be used to estimate correlations/attenuation factors when multiple 24HDRs are available. RESULTS: Overall, mean bias for sodium was -452 mg (95% CI: -646, -259), for potassium -315 mg (CI: -450, -179), and for the Na/K ratio -0.04 (CI: -0.15, 0.07, NS). Using 1 24HDR, the attenuation factor for sodium was 0.16 (CI: 0.09, 0.21), for potassium 0.25 (CI:0.16, 0.36), and for the Na/K ratio 0.20 (CI: 0.10, 0.25). The correlation for sodium was 0.27 (CI: 0.16, 0.37), for potassium 0.35 (CI: 0.26, 0.55), and for the Na/K ratio 0.27 (CI: 0.13, 0.32). CONCLUSIONS: Compared with 24HUE, using 24HDR underestimates mean sodium and potassium intake but is unbiased for the Na/K ratio. Additionally, using 24HDR as a measure of exposure in observational studies attenuates the true associations of sodium and potassium intake with health outcomes. |
Association of glucose levels in pregnancy with use of health care services
Vesco KK , Sharma AJ , Bulkley J , Terry Kimes M , Callaghan WM , England FLJ , Hornbrook MC . Diabetes Res Clin Pract 2019 152 146-155 AIMS: To determine whether women with abnormal gestational diabetes (GDM) screening test results short of frank GDM have increased health-services utilization compared to women with normal results. METHODS: We conducted a retrospective-cohort study among 29,999 women enrolled in Kaiser Permanente Northwest who completed GDM screening (two-step method:1-hour, 50-gram glucose-challenge test (GCT); 3-hour, 100-gram oral-glucose-tolerance test (OGTT)). Test results were categorized as normal GCT (referent, n=25,535), normal OGTT (n=2,246), abnormal OGTT but not GDM (n=1477), and GDM (n=741). Rate ratios (RRs) were calculated for utilization measures and analyses were age- and BMI-adjusted. RESULTS: Compared to women with normal GCT, rates for obstetrical ultrasound, noninvasive and invasive antenatal testing, and ambulatory visits to the obstetrics department were significantly greater among women with abnormal OGTT (RRs 1.2 [95%CI 1.1, 1.4], 1.3 [1.1, 1.4], 1.7 [1.3, 2.3], and 1.1 [1.1, 1.1], respectively) and GDM (RRs 1.8, 1.8, 2.0, and 1.3, respectively). Women with abnormal OGTT results were more likely to visit a dietician than women with normal GCT; RRs ranged from 4.0 [3.3, 4.9] for women with abnormal GCT but normal OGTT to 72.1 [64, 81] for women with GDM. CONCLUSIONS: Health-services utilization increased with severity of glucose result, even among women without GDM. |
Characterization of Novel Reoviruses [Wad Medani virus (Orbivirus) and Kundal (Coltivirus)] collected from Hyalomma antolicum ticks in India during CCHF surveillance.
Yadav PD , Whitmer SLM , Sarkale P , Ng TFF , Goldsmith CS , Nyayanit DA , Esona MD , Shrivastava-Ranjan P , Lakra R , Pardeshi P , Majumdar TD , Francis A , Klena JD , Nichol ST , Stroher U , Mourya D . J Virol 2019 93 (13) In 2011, ticks were collected from livestock following an outbreak of Crimean Congo Hemorrhagic fever (CCHF) in Gujarat state, India. CCHF-negative Hyalomma anatolicum tick pools were passaged for virus isolation, and two virus isolates were obtained, designated Karyana virus (KARYV) and Kundal virus (KUNDV) respectively. Traditional RT-PCR identification of known viruses was unsuccessful, but a next-generation sequencing approach identified KARYV and KUNDV as viruses in the Reoviridae family, Orbivirus, and Coltivirus genera, respectively. Viral genomes were de novo assembled, yielding 10 complete segments of KARYV and 12 nearly complete segments of KUNDV. The VP1 gene of KARYV shared a most recent common ancestor with Wad Medani virus (WMV), strain Ar495, and based on nucleotide identity we demonstrate that it is a novel WMV strain. The VP1 segment of KUNDV shares a common ancestor with Colorado tick fever virus, Eyach virus, Tai Forest reovirus and Tarumizu tick virus from the Coltivirus genus. Based on VP1, VP6, VP7, and VP12 nucleotide and amino acid identity, KUNDV is proposed to be a new species of Coltivirus Electron microscopy supported the classification of KARYV and KUNDV as reoviruses and identified replication morphology consistent with other Orbi- and Colti- viruses. The identification of novel tick-borne viruses carried by the CCHF vector is an important step in the characterization of their potential role in human and animal pathogenesis.Importance Ticks, mosquitoes, as well Culicoides, can transmit viruses in the Reoviridae family. With the help of next-generation sequencing (NGS), previously unreported reoviruses such as equine encephalosis virus, Wad Medani virus (WMV), Kammanvanpettai virus (KVPTV) and with this report, KARYV and KUNDV have been discovered and characterized in India. The isolation of KUNDV and KARYV from Hyalomma anatolicum, which is a known vector for zoonotic pathogens, such as Crimean Congo Hemorrhagic Fever virus, Babesia, Theileria and Anaplasma species, identifies arboviruses with the potential to transmit to humans. Characterization of these KUNDV and KARYV isolated from Hyalomma ticks is critical for the development of specific serological and molecular assays that can be used to determine the association of these viruses with disease in humans and livestock. |
Strengthening laboratory surveillance of viral pathogens: Experiences and lessons learned building next-generation sequencing capacity in Ghana.
Marine RL , Ntim NAA , Castro CJ , Attiku KO , Pratt D , Duker E , Agbosu E , Ng TFF , Gatei W , Obodai E , Odoom JK , Walker CL , Rota PA , Oberste MS , Ampofo WK , Balajee SA . Int J Infect Dis 2019 81 231-234 OBJECTIVES: To demonstrate the feasibility of applying next-generation sequencing (NGS) in medium-resource reference laboratories in Africa to enhance global disease surveillance. METHODS: A training program was developed to support implementation of NGS at Noguchi Memorial Institute for Medical Research (NMIMR), University of Ghana. The program was divided into two training stages, first at the Centers for Disease Control and Prevention (CDC) in Atlanta, GA, followed by on-site training at NMIMR for a larger cohort of scientists. RESULTS: Self-assessment scores for topics covered during the NGS training program were higher post-training relative to pre-training. During the NGS Training II session at NMIMR, six enterovirus isolates from acute flaccid paralysis cases in Ghana were successfully sequenced by trainees, including two echovirus 6, two echovirus 11 and one echovirus 13. Another genome was an uncommon type (EV-B84), which has not been reported in Africa since its initial discovery from a Cote d'Ivoire specimen in 2003. CONCLUSIONS: The success at NMIMR provides an example of how to approach transferring of NGS methods to international laboratories. There is great opportunity for collaboration between institutes that have genomics expertise to ensure effectiveness and long-term success of global NGS capacity building programs. |
Notes from the Field: Respiratory syncytial virus infections in a neonatal intensive care unit - Louisiana, December 2017
Washington EJ , Rose EB , Langley GE , Hand JP , Benowitz I , Gerber SI , Salinas AL , Terry AL , Tonzel JL , Sokol TM , Smith AT , Richardson GJ . MMWR Morb Mortal Wkly Rep 2019 68 (1) 20-21 In December 2017, the Louisiana Department of Health was notified of seven cases of respiratory syncytial virus (RSV) infection in a five-unit (units A–E), 84-bed neonatal intensive care unit (NICU) that included 66 individual infant rooms. The first case occurred in an infant who had been discharged postpartum from the NICU 30 days earlier and was readmitted for respiratory distress (day 0), approximately 2 weeks after the peak in reported RSV cases in Louisiana (mid-November) (1). The other six infants had at least one respiratory symptom while in the NICU postpartum. Upon identification of the first case, the facility implemented contact precautions for symptomatic infants, and NICU staff members were asked to report any respiratory symptoms. Nasopharyngeal specimens were obtained from infants who had rhinorrhea, cough, or nasal congestion. Nasopharyngeal swabs were also obtained from asymptomatic infants in two of the three units where the seven identified patients resided. A case was defined as laboratory-confirmed RSV infection in an NICU patient during December 2017. After consultation with CDC, a team of Louisiana Department of Health epidemiologists visited the facility 3 days after notification to review medical charts, observe infection control procedures, interview NICU staff members, and determine measures to prevent further transmission. |
Association of usual 24-h sodium excretion with measures of adiposity among adults in the United States: NHANES, 2014
Zhao L , Cogswell ME , Yang Q , Zhang Z , Onufrak S , Jackson SL , Chen TC , Loria CM , Wang CY , Wright JD , Terry AL , Merritt R , Ogden CL . Am J Clin Nutr 2019 109 (1) 139-147 Background: Both excessive sodium intake and obesity are risk factors for hypertension and cardiovascular disease. The association between sodium intake and obesity is unclear, with few studies assessing sodium intake using 24-h urine collection. Objectives: Our objective was to assess the association between usual 24-h sodium excretion and measures of adiposity among US adults. Methods: Cross-sectional data were analyzed from a sample of 730 nonpregnant participants aged 20-69 y who provided up to 2 complete 24-h urine specimens in the NHANES 2014 and had data on overweight or obesity [body mass index (kg/m2) >/=25] and central adiposity [waist circumference (WC): >88 cm for women, >102 cm for men]. Measurement error models were used to estimate usual sodium excretion, and multiple linear and logistic regression models were used to assess its associations with measures of adiposity, adjusting for sociodemographic, health, and dietary variables [i.e., energy intake or sugar-sweetened beverage (SSB) intake]. All analyses accounted for the complex survey sample design. Results: Unadjusted mean +/- SE usual sodium excretion was 3727 +/- 43.5 mg/d and 3145 +/- 55.0 mg/d among participants with and without overweight/obesity and 3653 +/- 58.1 mg/d and 3443 +/- 35.3 mg/d among participants with or without central adiposity, respectively. A 1000-mg/d higher sodium excretion was significantly associated with 3.8-units higher BMI (95% CI: 2.8, 4.8) and a 9.2-cm greater WC (95% CI: 6.9, 11.5 cm) adjusted for covariates. Compared with participants in the lowest quartile of sodium excretion, the adjusted prevalence ratios in the highest quartile were 1.93 (95% CI: 1.69, 2.20) for overweight/obesity and 2.07 (95% CI: 1.74, 2.46) for central adiposity. The associations also were significant when adjusting for SSBs, instead of energy, in models. Conclusions: Higher usual sodium excretion is associated with overweight/obesity and central adiposity among US adults. |
Characterization of the Genome Sequences of Enterovirus C109 from Two Respiratory Disease Cases in Florida, 2016.
Ng TFF , Yglesias JA , Stevenson-Yuen TA , Wolfe CM , Cone MR , Heberlein-Larson LA , Maher K , Rogers S , Chern SWW , Montmayeur A , Castro C , Nix WA . Microbiol Resour Announc 2018 7 (3) The genomic sequences of two enterovirus C109 isolates (EV-C109 USA/FL/2016-21003 and EV-C109 USA/FL/2016-21002) were obtained during two separate case investigations of respiratory disease in two children. This marks the first description of EV-C109 genomes in the United States. Copyright © 2018 Kyoui et al. |
- Page last reviewed:Feb 1, 2024
- Page last updated:May 06, 2024
- Content source:
- Powered by CDC PHGKB Infrastructure