Last data update: Apr 29, 2024. (Total: 46658 publications since 2009)
Records 1-13 (of 13 Records) |
Query Trace: van Zyl A[original query] |
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Recommendations on data sharing in HIV drug resistance research
Inzaule SC , Siedner MJ , Little SJ , Avila-Rios S , Ayitewala A , Bosch RJ , Calvez V , Ceccherini-Silberstein F , Charpentier C , Descamps D , Eshleman SH , Fokam J , Frenkel LM , Gupta RK , Ioannidis JPA , Kaleebu P , Kantor R , Kassaye SG , Kosakovsky Pond SL , Kouamou V , Kouyos RD , Kuritzkes DR , Lessells R , Marcelin AG , Mbuagbaw L , Minalga B , Ndembi N , Neher RA , Paredes R , Pillay D , Raizes EG , Rhee SY , Richman DD , Ruxrungtham K , Sabeti PC , Schapiro JM , Sirivichayakul S , Steegen K , Sugiura W , van Zyl GU , Vandamme AM , Wensing AMJ , Wertheim JO , Gunthard HF , Jordan MR , Shafer RW . PLoS Med 2023 20 (9) e1004293 Author summary • Human immunodeficiency virus (HIV) drug resistance has implications for antiretroviral treatment strategies and for containing the HIV pandemic because the development of HIV drug resistance leads to the requirement for antiretroviral drugs that may be less effective, less well-tolerated, and more expensive than those used in first-line regimens. • HIV drug resistance studies are designed to determine which HIV mutations are selected by antiretroviral drugs and, in turn, how these mutations affect antiretroviral drug susceptibility and response to future antiretroviral treatment regimens. • Such studies collectively form a vital knowledge base essential for monitoring global HIV drug resistance trends, interpreting HIV genotypic tests, and updating HIV treatment guidelines. • Although HIV drug resistance data are collected in many studies, such data are often not publicly shared, prompting the need to recommend best practices to encourage and standardize HIV drug resistance data sharing. • In contrast to other viruses, sharing HIV sequences from phylogenetic studies of transmission dynamics requires additional precautions as HIV transmission is criminalized in many countries and regions. • Our recommendations are designed to ensure that the data that contribute to HIV drug resistance knowledge will be available without undue hardship to those publishing HIV drug resistance studies and without risk to people living with HIV. |
Understanding COVID-19 vaccine hesitancy among K-12 staff, parents, and students: District of Columbia, February to April, 2022
Mark-Carew M , van Zyl A , Tatti KM , Chong M , Rose C , Sifre K , Jarris D , Still W , Aynalem G , Welton M , Thomas ES , Hall L , Samson ME . J Sch Health 2023 93 (12) 1079-1090 OBJECTIVE: Despite widespread availability of COVID-19 vaccines, millions of Americans have not received the recommended vaccine doses. In the District of Columbia (DC), COVID-19 vaccination rates are lowest among residents who are Non-Hispanic (NH) Black and among school-aged children. We assessed COVID-19 vaccine hesitancy among staff and parents of students in DC K-12 public and public charter schools. METHODS: We conducted a telephone-based survey from February 6 to April 16, 2022 to staff, students, and parents of students who participated in school-based COVID-19 screening testing. COVID-19-related survey items included: vaccination status, reasons for not getting vaccinated, perceived vaccine access, and trusted COVID-19 information sources. Utilizing time-to-event analyses, we evaluated differences across demographic groups. RESULTS: The interview response rate was 25.8% (308/1193). Most unvaccinated participants were NH Black and ages 5 to 11 years. Median time from vaccine eligibility to uptake was 236 days for NH Black participants vs. 10 days for NH White participants. Vaccine safety was the top concern among unvaccinated participants. Government and healthcare providers were the most trusted COVID-19 information sources. CONCLUSIONS: Differences in timing of vaccine uptake among respondents and greater vaccine hesitancy among NH Black participants compared to other racial/ethnic groups highlight a need for continued tailored outreach and communication using trusted sources to convey the importance, benefits, and safety of COVID-19 vaccination. |
Symptoms of depression, anxiety, and post-traumatic stress disorder, and suicidal ideation among school nurses in prekindergarten through grade 12 schools - United States, March 2022
Merkle SL , Welton M , van Zyl A , Chong M , Tanner A , Rose CE , Hertz M , Hill L , Leroy ZC , Sifre K , Thomas ES . J Sch Nurs 2022 39 (2) 10598405221131048 School nurses are integral to creating safe environments in U.S. schools. Many experienced increased work burden and stress during the COVID-19 pandemic. CDC collaborated with the National Association of School Nurses and the National Association of State School Nurse Consultants to distribute a 121-item online, anonymous survey to school nurses nationwide during March 7-30, 2022. Among the 7,971 respondents, symptoms of depression, anxiety and PTSD, and suicidal ideation were measured, and prevalence ratios were used to identify associations with demographics, workplace characteristics, and support. Results found high levels of work-related stressors and indicated that employment characteristics, COVID-19-related job duties, and other workplace stressors and supports affected school nurse mental health. The survey findings underscore the mental health challenges many school nurses experienced during the 2021/2022 school year. The findings can inform supportive policies and practices to reduce workplace stressors and increase workplace supports for school nurses. |
Primary resistance against integrase strand transfer inhibitors in integrase strand transfer inhibitor-naive patients failing first- and second-line ART in Tanzania.
Henerico S , Lyimo E , Makubi AN , Magesa D , Desderius B , Mueller A , Changalucha J , Kalluvya SE , Van Zyl G , Preiser W , Mshana SE , Kasang C . J Antimicrob Chemother 2022 77 (11) 3138-3143 INTRODUCTION: Sub-Saharan African countries are introducing integrase strand transfer inhibitors (INSTIs) in their ART programmes as the preferred first-line regimen, and dolutegravir is the INSTI of choice due to its potency, tolerability and high genetic barrier to resistance. Dolutegravir was introduced into the first-line ART regimen in Tanzania in 2019. However, there is a paucity of data on the occurrence of mutations in HIV lineages circulating in Tanzania. This study aimed to determine the prevalence of INSTI primary resistance mutations in Tanzanian patients exposed to ART but not INSTIs. METHODS: Plasma samples from 50 INSTI-naive patients failing first- or second-line ART [median (IQR) age: 40 (21.93-46.41) years; 68% women] were subjected to Sanger sequencing of the HIV integrase gene. Participants had been on ART for a median (IQR) duration of 7.32 (4.73-9.29) years, with 80% and 20% failing first- and second-line ART, respectively. RESULTS: No major INSTI mutations were found, but 2 (4%) participants had the accessory mutation T97A. Using the REGA HIV-1 subtyping tool, HIV subtype A1 (53.1%) was found to be dominant, followed by subtypes C (30.6%) and D (16.3%). CONCLUSIONS: This study found no current evidence for transmitted resistance against INSTIs among unexposed patients failing ART and supports the scale-up of INSTI-based regimens. However, the presence of accessory mutations calls for the surveillance of INSTI resistance mutations to ensure that the anticipated long-term desired outcomes are achieved. |
Test-to-Stay Implementation in Four Pre-K-12 School Districts.
Lammie SL , Ford L , Swanson M , Guinn AS , Kamitani E , van Zyl A , Rose CE , Marynak K , Shields J , Donovan CV , Holman EJ , Mark-Carew M , Welton M , Thomas ES , Neatherlin J . Pediatrics 2022 150 (4) OBJECTIVE: Globally, COVID-19 has affected how children learn. We evaluated the impact of Test to Stay (TTS) on secondary and tertiary transmission of SARS-CoV-2 and potential impact on in-person learning in four school districts in the United States from September 13-November 19, 2021. METHODS: Implementation of TTS varied across school districts. Data on index cases, school-based close contacts, TTS participation, and testing results were obtained from four school districts in diverse geographic regions. Descriptive statistics, secondary and tertiary attack risk, and a theoretical estimate of impact on in-person learning were calculated. RESULTS: Fifty-one schools in four school districts reported 374 COVID-19 index cases and 2,520 school-based close contacts eligible for TTS. The proportion participating in TTS ranged from 22%-79%. By district, the secondary attack risk (SAR) and tertiary attack risk (TAR) among TTS participants ranged between 2.2%-11.1% and 0%-17.6%, respectively. Nine clusters were identified among secondary cases and two among tertiary cases. The theoretical maximum number of days of in-person learning saved by using TTS was 976-4,650 days across jurisdictions. CONCLUSIONS: TTS preserves in-person learning days. Decisions to participate in TTS may have been influenced by ease of access to testing, communication between schools and families, testing logistics, and school resources. TAR determination became more complicated when numbers of close contacts increased. Minimizing exposure through continued implementation of layered prevention strategies is imperative. To ensure adequate resources for implementation of TTS, community transmission levels should be considered. |
Utility of a Test to Return Strategy to Identify Individuals with COVID-19 in the Pre-Kindergarten through Grade 12 School Setting - District of Columbia, January 2022.
Samson ME , Still WL , Mark-Carew M , Jarris DK , Idris A , van Zyl A , Addo D , Ashley P , Ike OJ , Thomas ES , Mangla AT , Nesbitt LS . Clin Infect Dis 2022 75 S231-S235 The highly transmissible SARS-CoV-2 Omicron variant led to increased hospitalizations, staffing shortages, and increased school closures. To reduce spread in school-aged children during the Omicron peak, the District of Columbia implemented a test-to-return strategy in public and public charter schools after a two-week break from in-person learning. |
Validation of the bag-mediated filtration system for environmental surveillance of poliovirus in Nairobi, Kenya
Fagnant-Sperati CS , Ren Y , Zhou NA , Komen E , Mwangi B , Hassan J , Chepkurui A , Nzunza R , Nyangao J , van Zyl WB , Wolfaardt M , Matsapola PN , Ngwana FB , Jeffries-Miles S , Coulliette-Salmond A , Peñaranda S , Vega E , Shirai JH , Kossik AL , Beck NK , Boyle DS , Burns CC , Taylor MB , Borus P , Scott Meschke J . J Appl Microbiol 2020 130 (3) 971-981 AIMS: This study compared the bag-mediated filtration system (BMFS) and standard WHO two-phase separation methods for poliovirus (PV) environmental surveillance, examined factors impacting PV detection, and monitored Sabin-like (SL) PV type 2 presence with withdrawal of oral polio vaccine type 2 (OPV2) in April 2016. METHODS AND RESULTS: Environmental samples were collected in Nairobi, Kenya (Sept 2015-Feb 2017), concentrated via BMFS and two-phase separation methods, then assayed using the WHO PV isolation algorithm and intratypic differentiation diagnostic screening kit. SL1, SL2, and SL3 were detected at higher rates in BMFS than two-phase samples (p<0.05). In BMFS samples, SL PV detection did not significantly differ with volume filtered, filtration time, or filter shipment time (p>0.05), while SL3 was detected less frequently with higher shipment temperatures (p=0.027). SL2 was detected more frequently before OPV2 withdrawal in BMFS and two-phase samples (p<1x10(-5) ). CONCLUSIONS: PV was detected at higher rates with the BMFS, a method that includes a secondary concentration step, than using the standard WHO two-phase method. SL2 disappearance from the environment was commensurate with OPV2 withdrawal. SIGNIFICANCE AND IMPACT OF THE STUDY: The BMFS offers comparable or improved PV detection under the conditions in this study, relative to the two-phase method. |
Feasibility of the bag-mediated filtration system for environmental surveillance of poliovirus in Kenya
Zhou NA , Fagnant-Sperati CS , Komen E , Mwangi B , Mukubi J , Nyangao J , Hassan J , Chepkurui A , Maina C , van Zyl WB , Matsapola PN , Wolfaardt M , Ngwana FB , Jeffries-Miles S , Coulliette-Salmond A , Penaranda S , Shirai JH , Kossik AL , Beck NK , Wilmouth R , Boyle DS , Burns CC , Taylor MB , Borus P , Meschke JS . Food Environ Virol 2019 12 (1) 35-47 The bag-mediated filtration system (BMFS) was developed to facilitate poliovirus (PV) environmental surveillance, a supplement to acute flaccid paralysis surveillance in PV eradication efforts. From April to September 2015, environmental samples were collected from four sites in Nairobi, Kenya, and processed using two collection/concentration methodologies: BMFS (> 3 L filtered) and grab sample (1 L collected; 0.5 L concentrated) with two-phase separation. BMFS and two-phase samples were analyzed for PV by the standard World Health Organization poliovirus isolation algorithm followed by intratypic differentiation. BMFS samples were also analyzed by a cell culture independent real-time reverse transcription polymerase chain reaction (rRT-PCR) and an alternative cell culture method (integrated cell culture-rRT-PCR with PLC/PRF/5, L20B, and BGM cell lines). Sabin polioviruses were detected in a majority of samples using BMFS (37/42) and two-phase separation (32/42). There was statistically more frequent detection of Sabin-like PV type 3 in samples concentrated with BMFS (22/42) than by two-phase separation (14/42, p = 0.035), possibly due to greater effective volume assayed (870 mL vs. 150 mL). Despite this effective volume assayed, there was no statistical difference in Sabin-like PV type 1 and Sabin-like PV type 2 detection between these methods (9/42 vs. 8/42, p = 0.80 and 27/42 vs. 32/42, p = 0.18, respectively). This study demonstrated that BMFS can be used for PV environmental surveillance and established a feasible study design for future research. |
Evaluation of the performance of three biomarker assays for recent HIV infection using a well-characterized HIV-1 subtype C incidence cohort
Gonese E , Kilmarx P , van Schalkwyk C , Grebe E , Mutasa K , Ntozini R , Parekh B , Dobbs T , Duong Pottinger Y , Masciotra S , Owen M , Nachega J , van Zyl G , Hargrove J . AIDS Res Hum Retroviruses 2019 35 (7) 615-627 BACKGROUND: Biomarkers for detecting early HIV infection and estimating HIV incidence should minimise False-Recent Rates (FRRs) while maximising Mean Duration of Recent Infection (MDRIs). We compared BED capture enzyme immunoassay (BED), Sedia Limiting Antigen Avidity EIA (LAg) and Bio-Rad avidity incident incidence (BRAI) assays using samples from Zimbabwean postpartum women infected with clade C HIV. METHODS: We calculated MDRIs using 590 samples from 351 seroconverting postpartum women, and FRRs using samples from 2,825 women known to be HIV-positive for >12 months. RESULTS: Antibody kinetics were more predictable with LAg and had higher precision compared to BED or BRAI. BRAI also exhibited more variability, and avidity reversal in some cases. For BED, LAg and BRAI, used alone or with viral load (VL), MDRI values in days were: BED - 188 and 170 at normalized optical density (ODn) 0.8; LAg - 104 and 100 at ODn cut-off 1.5; BRAI - 135 and 134 at Avidity Index cut-off 30%. Corresponding FRRs were: BRAI 1.1% and 1.0% and LAg 0.57% and 0.35%: these were 3.8 - 10.9 times lower than BED values of 4.8% and 3.8 Conclusion: BRAI and LAg have significantly lower FRRs and MDRIs than in published studies, and much lower than BED and could be used to estimate incidence in perinatal women and to measure population level HIV incidence in HIV control operations in Africa. BRAI and LAg have significantly lower FRRs and MDRIs than in published studies, and much lower than BED. These improved methods could be used to estimate incidence in perinatal women and to measure population level HIV incidence in HIV control operations in Africa. |
Mutational Correlates of Virological Failure in Individuals Receiving a WHO-Recommended Tenofovir-Containing First-Line Regimen: An International Collaboration.
Rhee SY , Varghese V , Holmes SP , Van Zyl GU , Steegen K , Boyd MA , Cooper DA , Nsanzimana S , Saravanan S , Charpentier C , de Oliveira T , Etiebet MA , Garcia F , Goedhals D , Gomes P , Gunthard HF , Hamers RL , Hoffmann CJ , Hunt G , Jiamsakul A , Kaleebu P , Kanki P , Kantor R , Kerschberger B , Marconi VC , D'Amour Ndahimana J , Ndembi N , Ngo-Giang-Huong N , Rokx C , Santoro MM , Schapiro JM , Schmidt D , Seu L , Sigaloff KC , Sirivichayakul S , Skhosana L , Sunpath H , Tang M , Yang C , Carmona S , Gupta RK , Shafer RW . EBioMedicine 2017 18 225-235 Tenofovir disoproxil fumarate (TDF) genotypic resistance defined by K65R/N and/or K70E/Q/G occurs in 20% to 60% of individuals with virological failure (VF) on a WHO-recommended TDF-containing first-line regimen. However, the full spectrum of reverse transcriptase (RT) mutations selected in individuals with VF on such a regimen is not known. To identify TDF regimen-associated mutations (TRAMs), we compared the proportion of each RT mutation in 2873 individuals with VF on a WHO-recommended first-line TDF-containing regimen to its proportion in a cohort of 50,803 antiretroviral-naive individuals. To identify TRAMs specifically associated with TDF-selection pressure, we compared the proportion of each TRAM to its proportion in a cohort of 5805 individuals with VF on a first-line thymidine analog-containing regimen. We identified 83 TRAMs including 33 NRTI-associated, 40 NNRTI-associated, and 10 uncommon mutations of uncertain provenance. Of the 33 NRTI-associated TRAMs, 12 - A62V, K65R/N, S68G/N/D, K70E/Q/T, L74I, V75L, and Y115F - were more common among individuals receiving a first-line TDF-containing compared to a first-line thymidine analog-containing regimen. These 12 TDF-selected TRAMs will be important for monitoring TDF-associated transmitted drug-resistance and for determining the extent of reduced TDF susceptibility in individuals with VF on a TDF-containing regimen. |
HIV-1 Drug Resistance Mutations: Potential Applications for Point-of-Care Genotypic Resistance Testing.
Rhee SY , Jordan MR , Raizes E , Chua A , Parkin N , Kantor R , Van Zyl GU , Mukui I , Hosseinipour MC , Frenkel LM , Ndembi N , Hamers RL , Rinke de Wit TF , Wallis CL , Gupta RK , Fokam J , Zeh C , Schapiro JM , Carmona S , Katzenstein D , Tang M , Aghokeng AF , De Oliveira T , Wensing AM , Gallant JE , Wainberg MA , Richman DD , Fitzgibbon JE , Schito M , Bertagnolio S , Yang C , Shafer RW . PLoS One 2015 10 (12) e0145772 The increasing prevalence of acquired and transmitted HIV-1 drug resistance is an obstacle to successful antiretroviral therapy (ART) in the low- and middle-income countries (LMICs) hardest hit by the HIV-1 pandemic. Genotypic drug resistance testing could facilitate the choice of initial ART in areas with rising transmitted drug resistance (TDR) and enable care-providers to determine which individuals with virological failure (VF) on a first- or second-line ART regimen require a change in treatment. An inexpensive near point-of-care (POC) genotypic resistance test would be useful in settings where the resources, capacity, and infrastructure to perform standard genotypic drug resistance testing are limited. Such a test would be particularly useful in conjunction with the POC HIV-1 viral load tests that are currently being introduced in LMICs. A POC genotypic resistance test is likely to involve the use of allele-specific point mutation assays for detecting drug-resistance mutations (DRMs). This study proposes that two major nucleoside reverse transcriptase inhibitor (NRTI)-associated DRMs (M184V and K65R) and four major NNRTI-associated DRMs (K103N, Y181C, G190A, and V106M) would be the most useful for POC genotypic resistance testing in LMIC settings. One or more of these six DRMs was present in 61.2% of analyzed virus sequences from ART-naive individuals with intermediate or high-level TDR and 98.8% of analyzed virus sequences from individuals on a first-line NRTI/NNRTI-containing regimen with intermediate or high-level acquired drug resistance. The detection of one or more of these DRMs in an ART-naive individual or in a individual with VF on a first-line NRTI/NNRTI-containing regimen may be considered an indication for a protease inhibitor (PI)-containing regimen or closer virological monitoring based on cost-effectiveness or country policy. |
Rotavirus G and P types circulating in the eastern region of Kenya: predominance of G9 and emergence of G12 genotypes.
Kiulia NM , Nyaga MM , Seheri ML , Wolfaardt M , van Zyl WB , Esona MD , Irimu G , Inoti M , Gatinu BW , Njenga PK , Taylor MB , Nyachieo A . Pediatr Infect Dis J 2014 33 Suppl 1 S85-8 BACKGROUND: The World Health Organization has recommended that rotavirus (RV) vaccines be included in all national immunization programs as part of a strategy to control RV-associated diarrheal diseases. Hospital-based surveillance of RV infection is therefore crucial in monitoring the impact pre- and post-vaccine introduction and also to document changes in genotype distribution. This study sought to determine the RV genotypes circulating in the eastern region of Kenya before introduction of the RV vaccine. METHODS: During September 2009 to August 2011, 500 stool samples were collected from children <5 years of age admitted for acute diarrhea in hospitals in the eastern region of Kenya and analyzed for the presence of group A RV using an enzyme immunoassay. G and P genotypes were determined using hemi-nested reverse transcriptase polymerase chain reaction. RESULTS: One hundred and eighty nine out of 500 (38%) samples analyzed were positive for rotavirus. The following G types were detected: G9 (50.9%), G1 (26.8%), G8 (12.1%), G12 (3.1%), G2 (0.6%), mixed G (1.3%) and 5.1% were G nontypeable. P types detected included: P[8] (63.7%), P[4] (12.1%), P[6] (4.5%), mixed P (7.6%) and 12.1% were P nontypeable. The most dominant strain was G9P[8] (35%), followed by G1P[8] (26.8%), G8P[4] (9.6%), G12P[6] (2.5%), G9P[6] (1.9%), G9P[4] (1.3%), G8P[8] (1.3%), and G2P[4] (0.6%). CONCLUSIONS: The present study demonstrates the recurring changing genotypes of RV circulating in Kenya, with genotypes G9, G1 and G8 being the dominant strains circulating in the eastern region of Kenya between 2009 and 2011. Additionally, G12 genotype was detected for the first time in Kenya. |
Parameters for sample size estimation from a group-randomized HIV prevention trial in HIV clinics in Sub-Saharan Africa
Zhang J , Pals SL , Medley A , Nichols C , Bachanas P , van Zyl D , Katuta F , Juma J . AIDS Behav 2013 18 (12) 2359-65 Sample size calculations for a group-randomized trial (GRT) require an estimate of the expected intraclass correlation coefficient (ICC). However, few ICC estimates from GRTs in HIV/AIDS research have been published, leaving investigators with little data on which to base expectations. We used data from a multi-country study to estimate ICCs for variables related to physical and mental health and HIV risk behaviors. ICCs for perceptions of physical and mental health tended to be higher than those for HIV risk behavior variables, which were higher than ICCs for CD4 count. Covariate adjustment for country and socio-demographic variables reduced most ICC estimates. For risk behavior variables, adjustment for country and socio-demographic variables reduced ICC estimates by as much as 84 %. Variability in ICC estimates has important implications for study design, as a larger ICC reduces power. ICC estimates presented in this analysis will allow more precise sample size estimates for future GRTs. |
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