Last data update: May 13, 2024. (Total: 46773 publications since 2009)
Records 1-30 (of 37 Records) |
Query Trace: McCauley J[original query] |
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Annual (2023) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria: kingdom Orthornavirae: phylum Negarnaviricota)
Kuhn JH , Abe J , Adkins S , Alkhovsky SV , Avšič-Županc T , Ayllón MA , Bahl J , Balkema-Buschmann A , Ballinger MJ , Kumar Baranwal V , Beer M , Bejerman N , Bergeron É , Biedenkopf N , Blair CD , Blasdell KR , Blouin AG , Bradfute SB , Briese T , Brown PA , Buchholz UJ , Buchmeier MJ , Bukreyev A , Burt F , Büttner C , Calisher CH , Cao M , Casas I , Chandran K , Charrel RN , Kumar Chaturvedi K , Chooi KM , Crane A , Dal Bó E , Carlos de la Torre J , de Souza WM , de Swart RL , Debat H , Dheilly NM , Di Paola N , Di Serio F , Dietzgen RG , Digiaro M , Drexler JF , Duprex WP , Dürrwald R , Easton AJ , Elbeaino T , Ergünay K , Feng G , Firth AE , Fooks AR , Formenty PBH , Freitas-Astúa J , Gago-Zachert S , Laura García M , García-Sastre A , Garrison AR , Gaskin TR , Gong W , Gonzalez JJ , de Bellocq J , Griffiths A , Groschup MH , Günther I , Günther S , Hammond J , Hasegawa Y , Hayashi K , Hepojoki J , Higgins CM , Hongō S , Horie M , Hughes HR , Hume AJ , Hyndman TH , Ikeda K , Jiāng D , Jonson GB , Junglen S , Klempa B , Klingström J , Kondō H , Koonin EV , Krupovic M , Kubota K , Kurath G , Laenen L , Lambert AJ , Lǐ J , Li JM , Liu R , Lukashevich IS , MacDiarmid RM , Maes P , Marklewitz M , Marshall SH , Marzano SL , McCauley JW , Mirazimi A , Mühlberger E , Nabeshima T , Naidu R , Natsuaki T , Navarro B , Navarro JA , Neriya Y , Netesov SV , Neumann G , Nowotny N , Nunes MRT , Ochoa-Corona FM , Okada T , Palacios G , Pallás V , Papa A , Paraskevopoulou S , Parrish CR , Pauvolid-Corrêa A , Pawęska JT , Pérez DR , Pfaff F , Plemper RK , Postler TS , Rabbidge LO , Radoshitzky SR , Ramos-González PL , Rehanek M , Resende RO , Reyes CA , Rodrigues TCS , Romanowski V , Rubbenstroth D , Rubino L , Runstadler JA , Sabanadzovic S , Sadiq S , Salvato MS , Sasaya T , Schwemmle M , Sharpe SR , Shi M , Shimomoto Y , Kavi Sidharthan V , Sironi M , Smither S , Song JW , Spann KM , Spengler JR , Stenglein MD , Takada A , Takeyama S , Tatara A , Tesh RB , Thornburg NJ , Tian X , Tischler ND , Tomitaka Y , Tomonaga K , Tordo N , Tu C , Turina M , Tzanetakis IE , Maria Vaira A , van den Hoogen B , Vanmechelen B , Vasilakis N , Verbeek M , von Bargen S , Wada J , Wahl V , Walker PJ , Waltzek TB , Whitfield AE , Wolf YI , Xia H , Xylogianni E , Yanagisawa H , Yano K , Ye G , Yuan Z , Zerbini FM , Zhang G , Zhang S , Zhang YZ , Zhao L , Økland AL . J Gen Virol 2023 104 (8) In April 2023, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by one new family, 14 new genera, and 140 new species. Two genera and 538 species were renamed. One species was moved, and four were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV. |
Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the US (preprint)
Cramer EY , Ray EL , Lopez VK , Bracher J , Brennen A , Castro Rivadeneira AJ , Gerding A , Gneiting T , House KH , Huang Y , Jayawardena D , Kanji AH , Khandelwal A , Le K , Mühlemann A , Niemi J , Shah A , Stark A , Wang Y , Wattanachit N , Zorn MW , Gu Y , Jain S , Bannur N , Deva A , Kulkarni M , Merugu S , Raval A , Shingi S , Tiwari A , White J , Abernethy NF , Woody S , Dahan M , Fox S , Gaither K , Lachmann M , Meyers LA , Scott JG , Tec M , Srivastava A , George GE , Cegan JC , Dettwiller ID , England WP , Farthing MW , Hunter RH , Lafferty B , Linkov I , Mayo ML , Parno MD , Rowland MA , Trump BD , Zhang-James Y , Chen S , Faraone SV , Hess J , Morley CP , Salekin A , Wang D , Corsetti SM , Baer TM , Eisenberg MC , Falb K , Huang Y , Martin ET , McCauley E , Myers RL , Schwarz T , Sheldon D , Gibson GC , Yu R , Gao L , Ma Y , Wu D , Yan X , Jin X , Wang YX , Chen Y , Guo L , Zhao Y , Gu Q , Chen J , Wang L , Xu P , Zhang W , Zou D , Biegel H , Lega J , McConnell S , Nagraj VP , Guertin SL , Hulme-Lowe C , Turner SD , Shi Y , Ban X , Walraven R , Hong QJ , Kong S , van de Walle A , Turtle JA , Ben-Nun M , Riley S , Riley P , Koyluoglu U , DesRoches D , Forli P , Hamory B , Kyriakides C , Leis H , Milliken J , Moloney M , Morgan J , Nirgudkar N , Ozcan G , Piwonka N , Ravi M , Schrader C , Shakhnovich E , Siegel D , Spatz R , Stiefeling C , Wilkinson B , Wong A , Cavany S , España G , Moore S , Oidtman R , Perkins A , Kraus D , Kraus A , Gao Z , Bian J , Cao W , Lavista Ferres J , Li C , Liu TY , Xie X , Zhang S , Zheng S , Vespignani A , Chinazzi M , Davis JT , Mu K , Pastore YPiontti A , Xiong X , Zheng A , Baek J , Farias V , Georgescu A , Levi R , Sinha D , Wilde J , Perakis G , Bennouna MA , Nze-Ndong D , Singhvi D , Spantidakis I , Thayaparan L , Tsiourvas A , Sarker A , Jadbabaie A , Shah D , Della Penna N , Celi LA , Sundar S , Wolfinger R , Osthus D , Castro L , Fairchild G , Michaud I , Karlen D , Kinsey M , Mullany LC , Rainwater-Lovett K , Shin L , Tallaksen K , Wilson S , Lee EC , Dent J , Grantz KH , Hill AL , Kaminsky J , Kaminsky K , Keegan LT , Lauer SA , Lemaitre JC , Lessler J , Meredith HR , Perez-Saez J , Shah S , Smith CP , Truelove SA , Wills J , Marshall M , Gardner L , Nixon K , Burant JC , Wang L , Gao L , Gu Z , Kim M , Li X , Wang G , Wang Y , Yu S , Reiner RC , Barber R , Gakidou E , Hay SI , Lim S , Murray C , Pigott D , Gurung HL , Baccam P , Stage SA , Suchoski BT , Prakash BA , Adhikari B , Cui J , Rodríguez A , Tabassum A , Xie J , Keskinocak P , Asplund J , Baxter A , Oruc BE , Serban N , Arik SO , Dusenberry M , Epshteyn A , Kanal E , Le LT , Li CL , Pfister T , Sava D , Sinha R , Tsai T , Yoder N , Yoon J , Zhang L , Abbott S , Bosse NI , Funk S , Hellewell J , Meakin SR , Sherratt K , Zhou M , Kalantari R , Yamana TK , Pei S , Shaman J , Li ML , Bertsimas D , Skali Lami O , Soni S , Tazi Bouardi H , Ayer T , Adee M , Chhatwal J , Dalgic OO , Ladd MA , Linas BP , Mueller P , Xiao J , Wang Y , Wang Q , Xie S , Zeng D , Green A , Bien J , Brooks L , Hu AJ , Jahja M , McDonald D , Narasimhan B , Politsch C , Rajanala S , Rumack A , Simon N , Tibshirani RJ , Tibshirani R , Ventura V , Wasserman L , O'Dea EB , Drake JM , Pagano R , Tran QT , Ho LST , Huynh H , Walker JW , Slayton RB , Johansson MA , Biggerstaff M , Reich NG . medRxiv 2021 2021.02.03.21250974 Short-term probabilistic forecasts of the trajectory of the COVID-19 pandemic in the United States have served as a visible and important communication channel between the scientific modeling community and both the general public and decision-makers. Forecasting models provide specific, quantitative, and evaluable predictions that inform short-term decisions such as healthcare staffing needs, school closures, and allocation of medical supplies. In 2020, the COVID-19 Forecast Hub (https://covid19forecasthub.org/) collected, disseminated, and synthesized hundreds of thousands of specific predictions from more than 50 different academic, industry, and independent research groups. This manuscript systematically evaluates 23 models that regularly submitted forecasts of reported weekly incident COVID-19 mortality counts in the US at the state and national level. One of these models was a multi-model ensemble that combined all available forecasts each week. The performance of individual models showed high variability across time, geospatial units, and forecast horizons. Half of the models evaluated showed better accuracy than a naïve baseline model. In combining the forecasts from all teams, the ensemble showed the best overall probabilistic accuracy of any model. Forecast accuracy degraded as models made predictions farther into the future, with probabilistic accuracy at a 20-week horizon more than 5 times worse than when predicting at a 1-week horizon. This project underscores the role that collaboration and active coordination between governmental public health agencies, academic modeling teams, and industry partners can play in developing modern modeling capabilities to support local, state, and federal response to outbreaks.Competing Interest StatementAV, MC, and APP report grants from Metabiota Inc outside the submitted work.Funding StatementFor teams that reported receiving funding for their work, we report the sources and disclosures below. CMU-TimeSeries: CDC Center of Excellence, gifts from Google and Facebook. CU-select: NSF DMS-2027369 and a gift from the Morris-Singer Foundation. COVIDhub: This work has been supported by the US Centers for Disease Control and Prevention (1U01IP001122) and the National Institutes of General Medical Sciences (R35GM119582). The content is solely the responsibility of the authors and does not necessarily represent the official views of CDC, NIGMS or the National Institutes of Health. Johannes Bracher was supported by the Helmholtz Foundation via the SIMCARD Information& Data Science Pilot Project. Tilmann Gneiting gratefully acknowledges support by the Klaus Tschira Foundation. DDS-NBDS: NSF III-1812699. EPIFORECASTS-ENSEMBLE1: Wellcome Trust (210758/Z/18/Z) GT_CHHS-COVID19: William W. George Endowment, Virginia C. and Joseph C. Mello Endowments, NSF DGE-1650044, NSF MRI 1828187, research cyberinfrastructure resources and services provided by the Partnership for an Advanced Computing Environment (PACE) at Georgia Tech, and the following benefactors at Georgia Tech: Andrea Laliberte, Joseph C. Mello, Richard Rick E. & Charlene Zalesky, and Claudia & Paul Raines GT-DeepCOVID: CDC MInD-Healthcare U01CK000531-Supplement. NSF (Expeditions CCF-1918770, CAREER IIS-2028586, RAPID IIS-2027862, Medium IIS-1955883, NRT DGE-1545362), CDC MInD program, ORNL and funds/computing resources from Georgia Tech and GTRI. IHME: This work was supported by the Bill & Melinda Gates Foundation, as well as funding from the state of Washington and the National Science Foundation (award no. FAIN: 2031096). IowaStateLW-STEM: Iowa State University Plant Sciences Institute Scholars Program, NSF DMS-1916204, NSF CCF-1934884, Laurence H. Baker Center for Bioinformatics and Biological Statistics. JHU_IDD-CovidSP: State of California, US Dept of Health and Human Services, US Dept of Homeland Security, US Office of Foreign Disaster Assistance, Johns Hopkins Health System, Office of the Dean at Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University Modeling and Policy Hub, Centers fo Disease Control and Prevention (5U01CK000538-03), University of Utah Immunology, Inflammation, & Infectious Disease Initiative (26798 Seed Grant). LANL-GrowthRate: LANL LDRD 20200700ER. MOBS-GLEAM_COVID: COVID Supplement CDC-HHS-6U01IP001137-01. NotreDame-mobility and NotreDame-FRED: NSF RAPID DEB 2027718 UA-EpiCovDA: NSF RAPID Grant # 2028401. UCSB-ACTS: NSF RAPID IIS 2029626. UCSD-NEU: Google Faculty Award, DARPA W31P4Q-21-C-0014, COVID Supplement CDC-HHS-6U01IP001137-01. UMass-MechBayes: NIGMS R35GM119582, NSF 1749854. UMich-RidgeTfReg: The University of Michigan Physics Department and the University of Michigan Office of Research.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:UMass-Amherst IRBAll 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.YesAll data and code referred to in the manuscript are publicly available. https://github.com/reichlab/covid19-forecast-hub/ https://github.com/reichlab/covidEnsembles https://zoltardata.com/project/44 |
Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution (preprint)
Huddleston J , Barnes JR , Rowe T , Xu X , Kondor R , Wentworth DE , Whittaker L , Ermetal B , Daniels RS , McCauley JW , Fujisaki S , Nakamura K , Kishida N , Watanabe S , Hasegawa H , Barr I , Subbarao K , Neher RA , Bedford T . bioRxiv 2020 2020.06.12.145151 Seasonal influenza virus A/H3N2 is a major cause of death globally. Vaccination remains the most effective preventative. Rapid mutation of hemagglutinin allows viruses to escape adaptive immunity. This antigenic drift necessitates regular vaccine updates. Effective vaccine strains need to represent H3N2 populations circulating one year after strain selection. Experts select strains based on experimental measurements of antigenic drift and predictions made by models from hemagglutinin sequences. We developed a novel influenza forecasting framework that integrates phenotypic measures of antigenic drift and functional constraint with previously published sequence-only fitness estimates. Forecasts informed by phenotypic measures of antigenic drift consistently outperformed previous sequence-only estimates, while sequence-only estimates of functional constraint surpassed more comprehensive experimentally-informed estimates. Importantly, the best models integrated estimates of both functional constraint and either antigenic drift phenotypes or recent population growth.Competing Interest StatementThe authors have declared no competing interest. |
2022 taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales.
Kuhn JH , Adkins S , Alkhovsky SV , Avi-upanc T , Aylln MA , Bahl J , Balkema-Buschmann A , Ballinger MJ , Bandte M , Beer M , Bejerman N , Bergeron , Biedenkopf N , Bigarr L , Blair CD , Blasdell KR , Bradfute SB , Briese T , Brown PA , Bruggmann R , Buchholz UJ , Buchmeier MJ , Bukreyev A , Burt F , Bttner C , Calisher CH , Candresse T , Carson J , Casas I , Chandran K , Charrel RN , Chiaki Y , Crane A , Crane M , Dacheux L , B ED , delaTorre JC , deLamballerie X , deSouza WM , deSwart RL , Dheilly NM , DiPaola N , DiSerio F , Dietzgen RG , Digiaro M , Drexler JF , Duprex WP , Drrwald R , Easton AJ , Elbeaino T , Ergnay K , Feng G , Feuvrier C , Firth AE , Fooks AR , Formenty PBH , Freitas-Asta J , Gago-Zachert S , Garca ML , Garca-Sastre A , Garrison AR , Godwin SE , Gonzalez JJ , deBellocq JG , Griffiths A , Groschup MH , Gnther S , Hammond J , Hepojoki J , Hierweger MM , Hong S , Horie M , Horikawa H , Hughes HR , Hume AJ , Hyndman TH , Jing D , Jonson GB , Junglen S , Kadono F , Karlin DG , Klempa B , Klingstrm J , Koch MC , Kond H , Koonin EV , Krsov J , Krupovic M , Kubota K , Kuzmin IV , Laenen L , Lambert AJ , L J , Li JM , Lieffrig F , Lukashevich IS , Luo D , Maes P , Marklewitz M , Marshall SH , Marzano SL , McCauley JW , Mirazimi A , Mohr PG , Moody NJG , Morita Y , Morrison RN , Mhlberger E , Naidu R , Natsuaki T , Navarro JA , Neriya Y , Netesov SV , Neumann G , Nowotny N , Ochoa-Corona FM , Palacios G , Pallandre L , Palls V , Papa A , Paraskevopoulou S , Parrish CR , Pauvolid-Corra A , Pawska JT , Prez DR , Pfaff F , Plemper RK , Postler TS , Pozet F , Radoshitzky SR , Ramos-Gonzlez PL , Rehanek M , Resende RO , Reyes CA , Romanowski V , Rubbenstroth D , Rubino L , Rumbou A , Runstadler JA , Rupp M , Sabanadzovic S , Sasaya T , Schmidt-Posthaus H , Schwemmle M , Seuberlich T , Sharpe SR , Shi M , Sironi M , Smither S , Song JW , Spann KM , Spengler JR , Stenglein MD , Takada A , Tesh RB , Tkov J , Thornburg NJ , Tischler ND , Tomitaka Y , Tomonaga K , Tordo N , Tsunekawa K , Turina M , Tzanetakis IE , Vaira AM , vandenHoogen B , Vanmechelen B , Vasilakis N , Verbeek M , vonBargen S , Wada J , Wahl V , Walker PJ , Whitfield AE , Williams JV , Wolf YI , Yamasaki J , Yanagisawa H , Ye G , Zhang YZ , kland AL . Arch Virol 2022 167 (12) 2857-2906 In March 2022, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by two new families (bunyaviral Discoviridae and Tulasviridae), 41 new genera, and 98 new species. Three hundred forty-nine species were renamed and/or moved. The accidentally misspelled names of seven species were corrected. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV. |
Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the United States.
Cramer EY , Ray EL , Lopez VK , Bracher J , Brennen A , Castro Rivadeneira AJ , Gerding A , Gneiting T , House KH , Huang Y , Jayawardena D , Kanji AH , Khandelwal A , Le K , Mühlemann A , Niemi J , Shah A , Stark A , Wang Y , Wattanachit N , Zorn MW , Gu Y , Jain S , Bannur N , Deva A , Kulkarni M , Merugu S , Raval A , Shingi S , Tiwari A , White J , Abernethy NF , Woody S , Dahan M , Fox S , Gaither K , Lachmann M , Meyers LA , Scott JG , Tec M , Srivastava A , George GE , Cegan JC , Dettwiller ID , England WP , Farthing MW , Hunter RH , Lafferty B , Linkov I , Mayo ML , Parno MD , Rowland MA , Trump BD , Zhang-James Y , Chen S , Faraone SV , Hess J , Morley CP , Salekin A , Wang D , Corsetti SM , Baer TM , Eisenberg MC , Falb K , Huang Y , Martin ET , McCauley E , Myers RL , Schwarz T , Sheldon D , Gibson GC , Yu R , Gao L , Ma Y , Wu D , Yan X , Jin X , Wang YX , Chen Y , Guo L , Zhao Y , Gu Q , Chen J , Wang L , Xu P , Zhang W , Zou D , Biegel H , Lega J , McConnell S , Nagraj VP , Guertin SL , Hulme-Lowe C , Turner SD , Shi Y , Ban X , Walraven R , Hong QJ , Kong S , van de Walle A , Turtle JA , Ben-Nun M , Riley S , Riley P , Koyluoglu U , DesRoches D , Forli P , Hamory B , Kyriakides C , Leis H , Milliken J , Moloney M , Morgan J , Nirgudkar N , Ozcan G , Piwonka N , Ravi M , Schrader C , Shakhnovich E , Siegel D , Spatz R , Stiefeling C , Wilkinson B , Wong A , Cavany S , España G , Moore S , Oidtman R , Perkins A , Kraus D , Kraus A , Gao Z , Bian J , Cao W , Lavista Ferres J , Li C , Liu TY , Xie X , Zhang S , Zheng S , Vespignani A , Chinazzi M , Davis JT , Mu K , Pastore YPiontti A , Xiong X , Zheng A , Baek J , Farias V , Georgescu A , Levi R , Sinha D , Wilde J , Perakis G , Bennouna MA , Nze-Ndong D , Singhvi D , Spantidakis I , Thayaparan L , Tsiourvas A , Sarker A , Jadbabaie A , Shah D , Della Penna N , Celi LA , Sundar S , Wolfinger R , Osthus D , Castro L , Fairchild G , Michaud I , Karlen D , Kinsey M , Mullany LC , Rainwater-Lovett K , Shin L , Tallaksen K , Wilson S , Lee EC , Dent J , Grantz KH , Hill AL , Kaminsky J , Kaminsky K , Keegan LT , Lauer SA , Lemaitre JC , Lessler J , Meredith HR , Perez-Saez J , Shah S , Smith CP , Truelove SA , Wills J , Marshall M , Gardner L , Nixon K , Burant JC , Wang L , Gao L , Gu Z , Kim M , Li X , Wang G , Wang Y , Yu S , Reiner RC , Barber R , Gakidou E , Hay SI , Lim S , Murray C , Pigott D , Gurung HL , Baccam P , Stage SA , Suchoski BT , Prakash BA , Adhikari B , Cui J , Rodríguez A , Tabassum A , Xie J , Keskinocak P , Asplund J , Baxter A , Oruc BE , Serban N , Arik SO , Dusenberry M , Epshteyn A , Kanal E , Le LT , Li CL , Pfister T , Sava D , Sinha R , Tsai T , Yoder N , Yoon J , Zhang L , Abbott S , Bosse NI , Funk S , Hellewell J , Meakin SR , Sherratt K , Zhou M , Kalantari R , Yamana TK , Pei S , Shaman J , Li ML , Bertsimas D , Skali Lami O , Soni S , Tazi Bouardi H , Ayer T , Adee M , Chhatwal J , Dalgic OO , Ladd MA , Linas BP , Mueller P , Xiao J , Wang Y , Wang Q , Xie S , Zeng D , Green A , Bien J , Brooks L , Hu AJ , Jahja M , McDonald D , Narasimhan B , Politsch C , Rajanala S , Rumack A , Simon N , Tibshirani RJ , Tibshirani R , Ventura V , Wasserman L , O'Dea EB , Drake JM , Pagano R , Tran QT , Ho LST , Huynh H , Walker JW , Slayton RB , Johansson MA , Biggerstaff M , Reich NG . Proc Natl Acad Sci U S A 2022 119 (15) e2113561119 SignificanceThis paper compares the probabilistic accuracy of short-term forecasts of reported deaths due to COVID-19 during the first year and a half of the pandemic in the United States. Results show high variation in accuracy between and within stand-alone models and more consistent accuracy from an ensemble model that combined forecasts from all eligible models. This demonstrates that an ensemble model provided a reliable and comparatively accurate means of forecasting deaths during the COVID-19 pandemic that exceeded the performance of all of the models that contributed to it. This work strengthens the evidence base for synthesizing multiple models to support public-health action. |
Cost-effectiveness of long-acting injectable HIV preexposure prophylaxis in the United States : A cost-effectiveness analysis
Neilan AM , Landovitz RJ , Le MH , Grinsztejn B , Freedberg KA , McCauley M , Wattananimitgul N , Cohen MS , Ciaranello AL , Clement ME , Reddy KP , Hyle EP , Paltiel AD , Walensky RP . Ann Intern Med 2022 175 (4) 479-489 BACKGROUND: The HIV Prevention Trials Network (HPTN) 083 trial demonstrated the superiority of long-acting injectable cabotegravir (CAB-LA) compared with oral emtricitabine-tenofovir disoproxil fumarate (F/TDF) for HIV preexposure prophylaxis (PrEP). OBJECTIVE: To identify the maximum price premium (that is, greatest possible price differential) that society should be willing to accept for the additional benefits of CAB-LA over tenofovir-based PrEP among men who have sex with men and transgender women (MSM/TGW) in the United States. DESIGN: Simulation, cost-effectiveness analysis. DATA SOURCES: Trial and published data, including estimated HIV incidence (5.32, 1.33, and 0.26 per 100 person-years for off PrEP, generic F/TDF and branded emtricitabine-tenofovir alafenamide (F/TAF), and CAB-LA, respectively); 28% 6-year PrEP retention. Annual base-case drug costs: $360 and $16800 for generic F/TDF and branded F/TAF. Fewer side effects with branded F/TAF versus generic F/TDF were assumed. TARGET POPULATION: 476700 MSM/TGW at very high risk for HIV (VHR). TIME HORIZON: 10 years. PERSPECTIVE: Health care system. INTERVENTION: CAB-LA versus generic F/TDF or branded F/TAF for HIV PrEP. OUTCOME MEASURES: Primary transmissions, quality-adjusted life-years (QALYs), costs (2020 U.S. dollars), incremental cost-effectiveness ratios (ICERs; U.S. dollars per QALY), maximum price premium for CAB-LA versus tenofovir-based PrEP. RESULTS OF BASE-CASE ANALYSIS: Compared with generic F/TDF (or branded F/TAF), CAB-LA increased life expectancy by 28000 QALYs (26000 QALYs) among those at VHR. Branded F/TAF cost more per QALY gained than generic F/TDF compared with no PrEP. At 10 years, CAB-LA could achieve an ICER of at most $100000 per QALY compared with generic F/TDF at a maximum price premium of $3700 per year over generic F/TDF (CAB-LA price <$4100 per year). RESULTS OF SENSITIVITY ANALYSIS: In a PrEP-eligible population at high risk for HIV, rather than at VHR (n = 1906800; off PrEP incidence: 1.54 per 100 person-years), CAB-LA could achieve an ICER of at most $100000 per QALY versus generic F/TDF at a maximum price premium of $1100 per year over generic F/TDF (CAB-LA price <$1500 per year). LIMITATION: Uncertain clinical and economic benefits of averting future transmissions. CONCLUSION: Effective oral PrEP limits the additional price society should be willing to pay for CAB-LA. PRIMARY FUNDING SOURCE: FHI 360; Eunice Kennedy Shriver National Institute of Child Health and Human Development; National Institute of Allergy and Infectious Diseases; National Heart, Lung, and Blood Institute; National Institute on Drug Abuse; the Reich HIV Scholar Award; and the Steve and Deborah Gorlin MGH Research Scholars Award. |
2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales.
Kuhn JH , Adkins S , Agwanda BR , Al Kubrusli R , Alkhovsky Aльxoвcкий Cepгeй Bлaдимиpoвич SV , Amarasinghe GK , Avšič-Županc T , Ayllón MA , Bahl J , Balkema-Buschmann A , Ballinger MJ , Basler CF , Bavari S , Beer M , Bejerman N , Bennett AJ , Bente DA , Bergeron É , Bird BH , Blair CD , Blasdell KR , Blystad DR , Bojko J , Borth WB , Bradfute S , Breyta R , Briese T , Brown PA , Brown JK , Buchholz UJ , Buchmeier MJ , Bukreyev A , Burt F , Büttner C , Calisher CH , Cao 曹孟籍 M , Casas I , Chandran K , Charrel RN , Cheng Q , Chiaki 千秋祐也 Y , Chiapello M , Choi IR , Ciuffo M , Clegg JCS , Crozier I , Dal Bó E , de la Torre JC , de Lamballerie X , de Swart RL , Debat H , Dheilly NM , Di Cicco E , Di Paola N , Di Serio F , Dietzgen RG , Digiaro M , Dolnik O , Drebot MA , Drexler JF , Dundon WG , Duprex WP , Dürrwald R , Dye JM , Easton AJ , Ebihara 海老原秀喜 H , Elbeaino T , Ergünay K , Ferguson HW , Fooks AR , Forgia M , Formenty PBH , Fránová J , Freitas-Astúa J , Fu 付晶晶 J , Fürl S , Gago-Zachert S , Gāo 高福 GF , García ML , García-Sastre A , Garrison AR , Gaskin T , Gonzalez JJ , Griffiths A , Goldberg TL , Groschup MH , Günther S , Hall RA , Hammond J , Han 韩彤 T , Hepojoki J , Hewson R , Hong 洪健 J , Hong 洪霓 N , Hongo 本郷誠治 S , Horie 堀江真行 M , Hu JS , Hu T , Hughes HR , Hüttner F , Hyndman TH , Ilyas M , Jalkanen R , Jiāng 姜道宏 D , Jonson GB , Junglen S , Kadono 上遠野冨士夫 F , Kaukinen KH , Kawate M , Klempa B , Klingström J , Kobinger G , Koloniuk I , Kondō 近藤秀樹 H , Koonin EV , Krupovic M , Kubota 久保田健嗣 K , Kurath G , Laenen L , Lambert AJ , Langevin SL , Lee B , Lefkowitz EJ , Leroy EM , Li 李邵蓉 S , Li 李龙辉 L , Lǐ 李建荣 J , Liu 刘华珍 H , Lukashevich IS , Maes P , de Souza WM , Marklewitz M , Marshall SH , Marzano SL , Massart S , McCauley JW , Melzer M , Mielke-Ehret N , Miller KM , Ming TJ , Mirazimi A , Mordecai GJ , Mühlbach HP , Mühlberger E , Naidu R , Natsuaki 夏秋知英 T , Navarro JA , Netesov Heтёcoв Cepгeй Bиктopoвич SV , Neumann G , Nowotny N , Nunes MRT , Olmedo-Velarde A , Palacios G , Pallás V , Pályi B , Papa Άννα Παπά A , Paraskevopoulou Σοφία Παρασκευοπούλου S , Park AC , Parrish CR , Patterson DA , Pauvolid-Corrêa A , Pawęska JT , Payne S , Peracchio C , Pérez DR , Postler TS , Qi 亓立莹 L , Radoshitzky SR , Resende RO , Reyes CA , Rima BK , Luna GR , Romanowski V , Rota P , Rubbenstroth D , Rubino L , Runstadler JA , Sabanadzovic S , Sall AA , Salvato MS , Sang R , Sasaya 笹谷孝英 T , Schulze AD , Schwemmle M , Shi 施莽 M , Shí 石晓宏 X , Shí 石正丽 Z , Shimomoto 下元祥史 Y , Shirako Y , Siddell SG , Simmonds P , Sironi M , Smagghe G , Smither S , Song 송진원 JW , Spann K , Spengler JR , Stenglein MD , Stone DM , Sugano J , Suttle CA , Tabata A , Takada 高田礼人 A , Takeuchi 竹内繁治 S , Tchouassi DP , Teffer A , Tesh RB , Thornburg NJ , Tomitaka 冨高保弘 Y , Tomonaga 朝長啓造 K , Tordo N , Torto B , Towner JS , Tsuda 津田新哉 S , Tu 涂长春 C , Turina M , Tzanetakis IE , Uchida J , Usugi 宇杉富雄 T , Vaira AM , Vallino M , van den Hoogen B , Varsani A , Vasilakis Νίκος Βασιλάκης N , Verbeek M , von Bargen S , Wada 和田治郎 J , Wahl V , Walker PJ , Wang 王林发 LF , Wang 王国平 G , Wang 王雁翔 Y , Wang 王亚琴 Y , Waqas M , Wèi 魏太云 T , Wen 温少华 S , Whitfield AE , Williams JV , Wolf YI , Wu 吴建祥 J , Xu 徐雷 L , Yanagisawa 栁澤広宣 H , Yang 杨彩霞 C , Yang 杨作坤 Z , Zerbini FM , Zhai 翟立峰 L , Zhang 张永振 YZ , Zhang 张松 S , Zhang 张靖国 J , Zhang 张哲 Z , Zhou 周雪平 X . Arch Virol 2021 166 (12) 3513-3566 In March 2021, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by four families (Aliusviridae, Crepuscuviridae, Myriaviridae, and Natareviridae), three subfamilies (Alpharhabdovirinae, Betarhabdovirinae, and Gammarhabdovirinae), 42 genera, and 200 species. Thirty-nine species were renamed and/or moved and seven species were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV. |
Cabotegravir for HIV prevention in cisgender men and transgender women
Landovitz RJ , Donnell D , Clement ME , Hanscom B , Cottle L , Coelho L , Cabello R , Chariyalertsak S , Dunne EF , Frank I , Gallardo-Cartagena JA , Gaur AH , Gonzales P , Tran HV , Hinojosa JC , Kallas EG , Kelley CF , Losso MH , Madruga JV , Middelkoop K , Phanuphak N , Santos B , Sued O , Valencia Huamaní J , Overton ET , Swaminathan S , Del Rio C , Gulick RM , Richardson P , Sullivan P , Piwowar-Manning E , Marzinke M , Hendrix C , Li M , Wang Z , Marrazzo J , Daar E , Asmelash A , Brown TT , Anderson P , Eshleman SH , Bryan M , Blanchette C , Lucas J , Psaros C , Safren S , Sugarman J , Scott H , Eron JJ , Fields SD , Sista ND , Gomez-Feliciano K , Jennings A , Kofron RM , Holtz TH , Shin K , Rooney JF , Smith KY , Spreen W , Margolis D , Rinehart A , Adeyeye A , Cohen MS , McCauley M , Grinsztejn B . N Engl J Med 2021 385 (7) 595-608 BACKGROUND: Safe and effective long-acting injectable agents for preexposure prophylaxis (PrEP) for human immunodeficiency virus (HIV) infection are needed to increase the options for preventing HIV infection. METHODS: We conducted a randomized, double-blind, double-dummy, noninferiority trial to compare long-acting injectable cabotegravir (CAB-LA, an integrase strand-transfer inhibitor [INSTI]) at a dose of 600 mg, given intramuscularly every 8 weeks, with daily oral tenofovir disoproxil fumarate-emtricitabine (TDF-FTC) for the prevention of HIV infection in at-risk cisgender men who have sex with men (MSM) and in at-risk transgender women who have sex with men. Participants were randomly assigned (1:1) to receive one of the two regimens and were followed for 153 weeks. HIV testing and safety evaluations were performed. The primary end point was incident HIV infection. RESULTS: The intention-to-treat population included 4566 participants who underwent randomization; 570 (12.5%) identified as transgender women, and the median age was 26 years (interquartile range, 22 to 32). The trial was stopped early for efficacy on review of the results of the first preplanned interim end-point analysis. Among 1698 participants from the United States, 845 (49.8%) identified as Black. Incident HIV infection occurred in 52 participants: 13 in the cabotegravir group (incidence, 0.41 per 100 person-years) and 39 in the TDF-FTC group (incidence, 1.22 per 100 person-years) (hazard ratio, 0.34; 95% confidence interval, 0.18 to 0.62). The effect was consistent across prespecified subgroups. Injection-site reactions were reported in 81.4% of the participants in the cabotegravir group and in 31.3% of those in the TDF-FTC group. In the participants in whom HIV infection was diagnosed after exposure to CAB-LA, INSTI resistance and delays in the detection of HIV infection were noted. No safety concerns were identified. CONCLUSIONS: CAB-LA was superior to daily oral TDF-FTC in preventing HIV infection among MSM and transgender women. Strategies are needed to prevent INSTI resistance in cases of CAB-LA PrEP failure. (Funded by the National Institute of Allergy and Infectious Diseases and others; HPTN 083 ClinicalTrials.gov number, NCT02720094.). |
Evaluation of phylogenetic methods for inferring the direction of HIV transmission: HPTN 052.
Zhang Y , Wymant C , Laeyendecker O , Grabowski MK , Hall M , Hudelson S , Piwowar-Manning E , McCauley M , Gamble T , Hosseinipour MC , Kumarasamy N , Hakim JG , Kumwenda J , Mills LA , Santos BR , Grinsztejn B , Pilotto JH , Chariyalertsak S , Makhema J , Chen YQ , Cohen MS , Fraser C , Eshleman SH . Clin Infect Dis 2021 72 (1) 30-37 BACKGROUND: Phylogenetic analysis can be used to assess human immunodeficiency virus (HIV) transmission in populations. We inferred the direction of HIV transmission using whole-genome HIV sequences from couples with known linked infection and known transmission direction. METHODS: Complete next-generation sequencing (NGS) data were obtained for 105 unique index-partner sample pairs from 32 couples enrolled in the HIV Prevention Trials Network (HPTN) 052 study (up to 2 samples/person). Index samples were obtained up to 5.5 years before partner infection; partner samples were obtained near the time of seroconversion. The bioinformatics method, phyloscanner, was used to infer transmission direction. Analyses were performed using samples from individual sample pairs, samples from all couples (1 sample/person; group analysis), and all available samples (multisample group analysis). Analysis was also performed using NGS data from defined regions of the HIV genome (gag, pol, env). RESULTS: Using whole-genome NGS data, transmission direction was inferred correctly (index to partner) for 98 of 105 (93.3%) of the individual sample pairs, 99 of 105 (94.3%) sample pairs using group analysis, and 31 of the 32 couples (96.9%) using multisample group analysis. There were no cases where the incorrect transmission direction (partner to index) was inferred. The accuracy of the method was higher with greater time between index and partner sample collection. Pol region sequences performed better than env or gag sequences for inferring transmission direction. CONCLUSIONS: We demonstrate the potential of a phylogenetic method to infer the direction of HIV transmission between 2 individuals using whole-genome and pol NGS data. |
Risk Factors for Severe Acute Respiratory Syndrome Coronavirus 2 Infection in Homeless Shelters in Chicago, Illinois-March-May, 2020.
Ghinai I , Davis ES , Mayer S , Toews KA , Huggett TD , Snow-Hill N , Perez O , Hayden MK , Tehrani S , Landi AJ , Crane S , Bell E , Hermes JM , Desai K , Godbee M , Jhaveri N , Borah B , Cable T , Sami S , Nozicka L , Chang YS , Jagadish A , Chee M , Thigpen B , Llerena C , Tran M , Surabhi DM , Smith ED , Remus RG , Staszcuk R , Figueroa E , Leo P , Detmer WM , Lyon E , Carreon S , Hoferka S , Ritger KA , Jasmin W , Nagireddy P , Seo JY , Fricchione MJ , Kerins JL , Black SR , Butler LM , Howard K , McCauley M , Fraley T , Arwady MA , Gretsch S , Cunningham M , Pacilli M , Ruestow PS , Mosites E , Avery E , Longcoy J , Lynch EB , Layden JE . Open Forum Infect Dis 2020 7 (11) ofaa477 BACKGROUND: People experiencing homelessness are at increased risk of coronavirus disease 2019 (COVID-19), but little is known about specific risk factors for infection within homeless shelters. METHODS: We performed widespread severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) polymerase chain reaction testing and collected risk factor information at all homeless shelters in Chicago with at least 1 reported case of COVID-19 (n = 21). Multivariable, mixed-effects log-binomial models were built to estimate adjusted prevalence ratios (aPRs) for SARS-CoV-2 infection for both individual- and facility-level risk factors. RESULTS: During March 1 to May 1, 2020, 1717 shelter residents and staff were tested for SARS-CoV-2; 472 (27%) persons tested positive. Prevalence of infection was higher for residents (431 of 1435, 30%) than for staff (41 of 282, 15%) (prevalence ratio = 2.52; 95% confidence interval [CI], 1.78-3.58). The majority of residents with SARS-CoV-2 infection (293 of 406 with available information about symptoms, 72%) reported no symptoms at the time of specimen collection or within the following 2 weeks. Among residents, sharing a room with a large number of people was associated with increased likelihood of infection (aPR for sharing with >20 people compared with single rooms = 1.76; 95% CI, 1.11-2.80), and current smoking was associated with reduced likelihood of infection (aPR = 0.71; 95% CI, 0.60-0.85). At the facility level, a higher proportion of residents leaving and returning each day was associated with increased prevalence (aPR = 1.08; 95% CI, 1.01-1.16), whereas an increase in the number of private bathrooms was associated with reduced prevalence (aPR for 1 additional private bathroom per 100 people = 0.92; 95% CI, 0.87-0.98). CONCLUSIONS: We identified a high prevalence of SARS-CoV-2 infections in homeless shelters. Reducing the number of residents sharing dormitories might reduce the likelihood of SARS-CoV-2 infection. When community transmission is high, limiting movement of persons experiencing homelessness into and out of shelters might also be beneficial. |
2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales.
Kuhn JH , Adkins S , Alioto D , Alkhovsky SV , Amarasinghe GK , Anthony SJ , Avšič-Županc T , Ayllón MA , Bahl J , Balkema-Buschmann A , Ballinger MJ , Bartonička T , Basler C , Bavari S , Beer M , Bente DA , Bergeron É , Bird BH , Blair C , Blasdell KR , Bradfute SB , Breyta R , Briese T , Brown PA , Buchholz UJ , Buchmeier MJ , Bukreyev A , Burt F , Buzkan N , Calisher CH , Cao M , Casas I , Chamberlain J , Chandran K , Charrel RN , Chen B , Chiumenti M , Choi IR , Clegg JCS , Crozier I , da Graça JV , Dal Bó E , Dávila AMR , de la Torre JC , de Lamballerie X , de Swart RL , Di Bello PL , Di Paola N , Di Serio F , Dietzgen RG , Digiaro M , Dolja VV , Dolnik O , Drebot MA , Drexler JF , Dürrwald R , Dufkova L , Dundon WG , Duprex WP , Dye JM , Easton AJ , Ebihara H , Elbeaino T , Ergünay K , Fernandes J , Fooks AR , Formenty PBH , Forth LF , Fouchier RAM , Freitas-Astúa J , Gago-Zachert S , Gāo GF , García ML , García-Sastre A , Garrison AR , Gbakima A , Goldstein T , Gonzalez JJ , Griffiths A , Groschup MH , Günther S , Guterres A , Hall RA , Hammond J , Hassan M , Hepojoki J , Hepojoki S , Hetzel U , Hewson R , Hoffmann B , Hongo S , Höper D , Horie M , Hughes HR , Hyndman TH , Jambai A , Jardim R , Jiāng D , Jin Q , Jonson GB , Junglen S , Karadağ S , Keller KE , Klempa B , Klingström J , Kobinger G , Kondō H , Koonin EV , Krupovic M , Kurath G , Kuzmin IV , Laenen L , Lamb RA , Lambert AJ , Langevin SL , Lee B , Lemos ERS , Leroy EM , Li D , Lǐ J , Liang M , Liú W , Liú Y , Lukashevich IS , Maes P , Marciel de Souza W , Marklewitz M , Marshall SH , Martelli GP , Martin RR , Marzano SL , Massart S , McCauley JW , Mielke-Ehret N , Minafra A , Minutolo M , Mirazimi A , Mühlbach HP , Mühlberger E , Naidu R , Natsuaki T , Navarro B , Navarro JA , Netesov SV , Neumann G , Nowotny N , Nunes MRT , Nylund A , Økland AL , Oliveira RC , Palacios G , Pallas V , Pályi B , Papa A , Parrish CR , Pauvolid-Corrêa A , Pawęska JT , Payne S , Pérez DR , Pfaff F , Radoshitzky SR , Rahman AU , Ramos-González PL , Resende RO , Reyes CA , Rima BK , Romanowski V , Robles Luna G , Rota P , Rubbenstroth D , Runstadler JA , Ruzek D , Sabanadzovic S , Salát J , Sall AA , Salvato MS , Sarpkaya K , Sasaya T , Schwemmle M , Shabbir MZ , Shí X , Shí Z , Shirako Y , Simmonds P , Širmarová J , Sironi M , Smither S , Smura T , Song JW , Spann KM , Spengler JR , Stenglein MD , Stone DM , Straková P , Takada A , Tesh RB , Thornburg NJ , Tomonaga K , Tordo N , Towner JS , Turina M , Tzanetakis I , Ulrich RG , Vaira AM , van den Hoogen B , Varsani A , Vasilakis N , Verbeek M , Wahl V , Walker PJ , Wang H , Wang J , Wang X , Wang LF , Wèi T , Wells H , Whitfield AE , Williams JV , Wolf YI , Wú Z , Yang X , Yáng X , Yu X , Yutin N , Zerbini FM , Zhang T , Zhang YZ , Zhou G , Zhou X . Arch Virol 2020 165 (12) 3023-3072 In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted, ten were moved and renamed, and 30 species were renamed. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV. |
Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution.
Huddleston J , Barnes JR , Rowe T , Xu X , Kondor R , Wentworth DE , Whittaker L , Ermetal B , Daniels RS , McCauley JW , Fujisaki S , Nakamura K , Kishida N , Watanabe S , Hasegawa H , Barr I , Subbarao K , Barrat-Charlaix P , Neher RA , Bedford T . Elife 2020 9 Seasonal influenza virus A/H3N2 is a major cause of death globally. Vaccination remains the most effective preventative. Rapid mutation of hemagglutinin allows viruses to escape adaptive immunity. This antigenic drift necessitates regular vaccine updates. Effective vaccine strains need to represent H3N2 populations circulating one year after strain selection. Experts select strains based on experimental measurements of antigenic drift and predictions made by models from hemagglutinin sequences. We developed a novel influenza forecasting framework that integrates phenotypic measures of antigenic drift and functional constraint with previously published sequence-only fitness estimates. Forecasts informed by phenotypic measures of antigenic drift consistently outperformed previous sequence- only estimates, while sequence-only estimates of functional constraint surpassed more comprehensive experimentally-informed estimates. Importantly, the best models integrated estimates of both functional constraint and either antigenic drift phenotypes or recent population growth. |
Prevention of sexual violence among college students: Current challenges and future directions
Bonar EE , DeGue S , Abbey A , Coker AL , Lindquist CH , McCauley HL , Miller E , Senn CY , Thompson MP , Ngo QM , Cunningham RM , Walton MA . J Am Coll Health 2020 70 (2) 1-14 Objective: Preventing sexual violence among college students is a public health priority. This paper was catalyzed by a summit convened in 2018 to review the state of the science on campus sexual violence prevention. We summarize key risk and vulnerability factors and campus-based interventions, and provide directions for future research pertaining to campus sexual violence. Results and Conclusions: Although studies have identified risk factors for campus sexual violence, longitudinal research is needed to examine time-varying risk factors across social ecological levels (individual, relationship, campus context/broader community and culture) and data are particularly needed to identify protective factors. In terms of prevention, promising individual and relational level interventions exist, including active bystander, resistance, and gender transformative approaches; however, further evidence-based interventions are needed, particularly at the community-level, with attention to vulnerability factors and inclusion for marginalized students. |
Pandemic potential of highly pathogenic avian influenza clade 2.3.4.4 A(H5) viruses
Yamaji R , Saad MD , Davis CT , Swayne DE , Wang D , Wong FYK , McCauley JW , Peiris JSM , Webby RJ , Fouchier RAM , Kawaoka Y , Zhang W . Rev Med Virol 2020 30 (3) e2099 The panzootic caused by A/goose/Guangdong/1/96-lineage highly pathogenic avian influenza (HPAI) A(H5) viruses has occurred in multiple waves since 1996. From 2013 onwards, clade 2.3.4.4 viruses of subtypes A(H5N2), A(H5N6), and A(H5N8) emerged to cause panzootic waves of unprecedented magnitude among avian species accompanied by severe losses to the poultry industry around the world. Clade 2.3.4.4 A(H5) viruses have expanded in distinct geographical and evolutionary pathways likely via long distance migratory bird dispersal onto several continents and by poultry trade among neighboring countries. Coupled with regional circulation, the viruses have evolved further by reassorting with local viruses. As of February 2019, there have been 23 cases of humans infected with clade 2.3.4.4 H5N6 viruses, 16 (70%) of which had fatal outcomes. To date, no HPAI A(H5) virus has caused sustainable human-to-human transmission. However, due to the lack of population immunity in humans and ongoing evolution of the virus, there is a continuing risk that clade 2.3.4.4 A(H5) viruses could cause an influenza pandemic if the ability to transmit efficiently among humans was gained. Therefore, multisectoral collaborations among the animal, environmental, and public health sectors are essential to conduct risk assessments and develop countermeasures to prevent disease and to control spread. In this article, we describe an assessment of the likelihood of clade 2.3.4.4 A(H5) viruses gaining human-to-human transmissibility and impact on human health should such human-to-human transmission occur. This structured analysis assessed properties of the virus, attributes of the human population, and ecology and epidemiology of these viruses in animal hosts. |
Phylogenetic methods inconsistently predict direction of HIV transmission among heterosexual pairs in the HPTN052 cohort.
Rose R , Hall M , Redd AD , Lamers S , Barbier AE , Porcella SF , Hudelson SE , Piwowar-Manning E , McCauley M , Gamble T , Wilson EA , Kumwenda J , Hosseinipour MC , Hakim JG , Kumarasamy N , Chariyalertsak S , Pilotto JH , Grinsztejn B , Mills LA , Makhema J , Santos BR , Chen YQ , Quinn TC , Fraser C , Cohen MS , Eshleman SH , Laeyendecker O . J Infect Dis 2018 220 (9) 1406-1413 Background: We evaluated use of phylogenetic methods to predict the direction of HIV transmission. Methods: For 33 index-partner pairs with genetically-linked infection, samples were collected from partners and indexes close to time of partners' seroconversion (SC); 31 indexes also had an earlier sample. Phylogenies were inferred using env next-generation sequences (one tree per pair/subtype). Direction of transmission (DoT) predicted from each tree was classified as correct or incorrect based on which sequences (index or partner) were closest to the root. DoT was also assessed using maximum-parsimony to infer ancestral node states for 100 bootstrap trees. Results: DoT was predicted correctly for both single pair and subtype-specific trees in 22 pairs (67%) using SC samples and 23 pairs (74%) using early index samples. DoT was predicted incorrectly for four pairs (15%) using SC or early index samples. In the bootstrap analysis, DoT was predicted correctly for 18 pairs (55%) using SC samples and 24 pairs (73%) using early index samples. DoT was predicted incorrectly for seven pairs (21%) using SC samples and four pairs (13%) using early index samples. Conclusions: Phylogenetic methods based solely on tree topology of HIV env sequences, particularly without consideration of phylogenetic uncertainty, may be insufficient for determining DoT. |
Cell culture-derived influenza vaccines in the severe 2017-2018 epidemic season: a step towards improved influenza vaccine effectiveness
Barr IG , Donis RO , Katz JM , McCauley JW , Odagiri T , Trusheim H , Tsai TF , Wentworth DE . NPJ Vaccines 2018 3 44 The 2017-2018 seasonal influenza epidemics were severe in the US and Australia where the A(H3N2) subtype viruses predominated. Although circulating A(H3N2) viruses did not differ antigenically from that recommended by the WHO for vaccine production, overall interim vaccine effectiveness estimates were below historic averages (33%) for A(H3N2) viruses. The majority (US) or all (Australian) vaccine doses contained multiple amino-acid changes in the hemagglutinin protein, resulting from the necessary adaptation of the virus to embryonated hen's eggs used for most vaccine manufacturing. Previous reports have suggested a potential negative impact of egg-driven substitutions on vaccine performance. With BARDA support, two vaccines licensed in the US are produced in cell culture: recombinant influenza vaccine (RIV, Flublok) manufactured in insect cells and inactivated mammalian cell-grown vaccine (ccIIV, Flucelvax). Quadrivalent ccIIV (ccIIV4) vaccine for the 2017-2018 influenza season was produced using an A(H3N2) seed virus propagated exclusively in cell culture and therefore lacking egg adaptative changes. Sufficient ccIIV doses were distributed (but not RIV doses) to enable preliminary estimates of its higher effectiveness relative to the traditional egg-based vaccines, with study details pending. The increased availability of comparative product-specific vaccine effectiveness estimates for cell-based and egg-based vaccines may provide critical clues to inform vaccine product improvements moving forward. |
HIV drug resistance in adults receiving early versus delayed antiretroviral therapy: HPTN 052
Palumbo PJ , Fogel JM , Hudelson SE , Wilson EA , Hart S , Hovind L , Piwowar-Manning E , Wallis C , Papathanasopoulos MA , Morgado MG , Saravanan S , Tripathy S , Eron JJ , Gallant JE , Mph , McCauley M , Gamble T , Hosseinipour MC , Kumarasamy N , Hakim JG , Pilotto JH , Kumwenda J , Akelo V , Godbole SV , Santos BR , Grinsztejn B , Panchia R , Chariyalertsak S , Makhema J , Badal-Faesen S , Chen YQ , Cohen MS , Eshleman SH . J Acquir Immune Defic Syndr 2017 77 (5) 484-491 INTRODUCTION: We evaluated HIV drug resistance in adults who received early versus delayed antiretroviral therapy (ART) in a multi-national trial (HPTN 052, enrollment 2005-2010). In HPTN 052, 1,763 index participants were randomized to start ART at a CD4 cell count of 350-550 cells/mm3 (early ART arm) or <250 cells/mm3 (delayed ART arm). In May 2011, interim study results showed benefit of early ART, and all participants were offered ART regardless of CD4 cell count; the study ended in 2015. METHODS: Virologic failure was defined as two consecutive viral loads >1,000 copies/mL >24 weeks after ART initiation. Drug resistance testing was performed for pre-treatment (baseline) and failure samples from participants with virologic failure. RESULTS: HIV genotyping results were obtained for 211/249 participants (128 early ART arm; 83 delayed ART arm) with virologic failure. Drug resistance was detected in 4.7% of participants at baseline; 35.5% had new resistance at failure. In univariate analysis, the frequency of new resistance at failure was lower among participants in the early ART arm (compared to delayed ART arm, p=0.06; compared to delayed ART arm with ART initiation before May 2011, p=0.032). In multivariate analysis, higher baseline viral load (p=0.0008) and ART regimen (efavirenz/lamivudine/zidovudine compared to other regimens, p=0.024) were independently associated with higher risk of new resistance at failure. CONCLUSIONS: In HPTN 052, the frequency of new drug resistance at virologic failure was lower in adults with early ART initiation. The main factor associated with reduced drug resistance with early ART was lower baseline viral load. |
Virologic outcomes in early antiretroviral treatment: HPTN 052
Eshleman SH , Wilson EA , Zhang XC , Ou SS , Piwowar-Manning E , Eron JJ , McCauley M , Gamble T , Gallant JE , Hosseinipour MC , Kumarasamy N , Hakim JG , Kalonga B , Pilotto JH , Grinsztejn B , Godbole SV , Chotirosniramit N , Santos BR , Shava E , Mills LA , Panchia R , Mwelase N , Mayer KH , Chen YQ , Cohen MS , Fogel JM . HIV Clin Trials 2017 18 (3) 1-10 INTRODUCTION: The HIV Prevention Trials Network (HPTN) 052 trial demonstrated that early antiretroviral therapy (ART) prevented 93% of HIV transmission events in serodiscordant couples. Some linked infections were observed shortly after ART initiation or after virologic failure. OBJECTIVE: To evaluate factors associated with time to viral suppression and virologic failure in participants who initiated ART in HPTN 052. METHODS: 1566 participants who had a viral load (VL) > 400 copies/mL at enrollment were included in the analyses. This included 832 in the early ART arm (CD4 350-550 cells/mm3 at ART initiation) and 734 in the delayed ART arm (204 with a CD4 < 250 cells/mm3 at ART initiation; 530 with any CD4 at ART initiation). Viral suppression was defined as two consecutive VLs ≤ 400 copies/mL after ART initiation; virologic failure was defined as two consecutive VLs > 1000 copies/mL > 24 weeks after ART initiation. RESULTS: Overall, 93% of participants achieved viral suppression by 12 months. The annual incidence of virologic failure was 3.6%. Virologic outcomes were similar in the two study arms. Longer time to viral suppression was associated with younger age, higher VL at ART initiation, and region (Africa vs. Asia). Virologic failure was strongly associated with younger age, lower educational level, and lack of suppression by three months; lower VL and higher CD4 at ART initiation were also associated with virologic failure. CONCLUSIONS: Several clinical and demographic factors were identified that were associated with longer time to viral suppression and virologic failure. Recognition of these factors may help optimize ART for HIV treatment and prevention. |
Improving the selection and development of influenza vaccine viruses - Report of a WHO informal consultation on improving influenza vaccine virus selection, Hong Kong SAR, China, 18-20 November 2015.
Hampson A , Barr I , Cox N , Donis RO , Hirve S , Jernigan D , Katz J , McCauley J , Motta F , Odagiri T , Tami JS , Waddell A , Webby R , Ziegler T , Zhang W . Vaccine 2017 35 (8) 1104-1109 Since 2010 the WHO has held a series of informal consultations to explore ways of improving the currently highly complex and time-pressured influenza vaccine virus selection and development process. In November 2015 experts from around the world met to review the current status of efforts in this field. Discussion topics included strengthening influenza surveillance activities to increase the availability of candidate vaccine viruses and improve the extent, timeliness and quality of surveillance data. Consideration was also given to the development and potential application of newer laboratory assays to better characterize candidate vaccine viruses, the potential importance of antibodies directed against influenza virus neuraminidase, and the role of vaccine effectiveness studies. Advances in next generation sequencing and whole genome sequencing of influenza viruses were also discussed, along with associated developments in synthetic genomics technologies, evolutionary analysis and predictive mathematical modelling. Discussions were also held on the late emergence of an antigenic variant influenza A(H3N2) virus in mid-2014 that could not be incorporated in time into the 2014-15 northern hemisphere vaccine. There was broad recognition that given the current highly constrained influenza vaccine development and production timeline it would remain impossible to incorporate any variant virus which emerged significantly long after the relevant WHO biannual influenza vaccine composition meetings. Discussions were also held on the development of pandemic and broadly protective vaccines, and on associated regulatory and manufacturing requirements and constraints. With increasing awareness of the health and economic burdens caused by seasonal influenza, the ever-present threat posed by zoonotic influenza viruses, and the significant impact of the 2014-15 northern hemisphere seasonal influenza vaccine mismatch, this consultation provided a very timely opportunity to share developments and exchange views. In all areas, a renewed and strengthened emphasis was placed on developing concrete and measurable actions and identifying the key stakeholders responsible for their implementation. |
Selection of antigenically advanced variants of seasonal influenza viruses
Li C , Hatta M , Burke DF , Ping J , Zhang Y , Ozawa M , Taft AS , Das SC , Hanson AP , Song J , Imai M , Wilker PR , Watanabe T , Watanabe S , Ito M , Iwatsuki-Horimoto K , Russell CA , James SL , Skepner E , Maher EA , Neumann G , Klimov AI , Kelso A , McCauley J , Wang D , Shu Y , Odagiri T , Tashiro M , Xu X , Wentworth DE , Katz JM , Cox NJ , Smith DJ , Kawaoka Y . Nat Microbiol 2016 1 (6) 16058 Influenza viruses mutate frequently, necessitating constant updates of vaccine viruses. To establish experimental approaches that may complement the current vaccine strain selection process, we selected antigenic variants from human H1N1 and H3N2 influenza virus libraries possessing random mutations in the globular head of the haemagglutinin protein (which includes the antigenic sites) by incubating them with human and/or ferret convalescent sera to human H1N1 and H3N2 viruses. We also selected antigenic escape variants from human viruses treated with convalescent sera and from mice that had been previously immunized against human influenza viruses. Our pilot studies with past influenza viruses identified escape mutants that were antigenically similar to variants that emerged in nature, establishing the feasibility of our approach. Our studies with contemporary human influenza viruses identified escape mutants before they caused an epidemic in 2014-2015. This approach may aid in the prediction of potential antigenic escape variants and the selection of future vaccine candidates before they become widespread in nature. |
Treatment as Prevention: Characterization of partner infections in the HIV Prevention Trials Network 052 trial.
Eshleman SH , Hudelson SE , Redd AD , Swanstrom R , Ou SS , Zhang XC , Ping LH , Piwowar-Manning E , Porcella SF , Sievers MF , Martens CA , Bruno D , Dukhovlinova E , McCauley M , Gamble T , Fogel JM , Sabin D , Quinn TC , Gunde L , Maliwichi M , Nhando N , Akelo V , Moyo S , Panchia R , Kumarasamy N , Chotirosniramit N , Goncalves de Melo M , Pilotto J , Grinsztejn B , Mayer K , Chen YQ , Hughes JP , Cohen MS . J Acquir Immune Defic Syndr 2016 74 (1) 112-116 HIV Prevention Trials Network (HPTN) 052 demonstrated that antiretroviral therapy (ART) prevents HIV transmission in serodiscordant couples. HIV from index-partner pairs was analyzed to determine the genetic linkage status of partner infections. Forty-six infections were classified as linked, indicating that the index was the likely source of the partner's infection. Lack of viral suppression and higher index viral load were associated with linked infection. Eight linked infections were diagnosed after the index started ART: four near the time of ART initiation and four after ART failure. Linked infections were not observed when the index participant was stably suppressed on ART. |
Antiretroviral Therapy for the Prevention of HIV-1 Transmission.
Cohen MS , Chen YQ , McCauley M , Gamble T , Hosseinipour MC , Kumarasamy N , Hakim JG , Kumwenda J , Grinsztejn B , Pilotto JH , Godbole SV , Chariyalertsak S , Santos BR , Mayer KH , Hoffman IF , Eshleman SH , Piwowar-Manning E , Cottle L , Zhang XC , Makhema J , Mills LA , Panchia R , Faesen S , Eron J , Gallant J , Havlir D , Swindells S , Elharrar V , Burns D , Taha TE , Nielsen-Saines K , Celentano DD , Essex M , Hudelson SE , Redd AD , Fleming TR . N Engl J Med 2016 375 (9) 830-9 Background An interim analysis of data from the HIV Prevention Trials Network (HPTN) 052 trial showed that antiretroviral therapy (ART) prevented more than 96% of genetically linked infections caused by human immunodeficiency virus type 1 (HIV-1) in serodiscordant couples. ART was then offered to all patients with HIV-1 infection (index participants). The study included more than 5 years of follow-up to assess the durability of such therapy for the prevention of HIV-1 transmission. Methods We randomly assigned 1763 index participants to receive either early or delayed ART. In the early-ART group, 886 participants started therapy at enrollment (CD4+ count, 350 to 550 cells per cubic millimeter). In the delayed-ART group, 877 participants started therapy after two consecutive CD4+ counts fell below 250 cells per cubic millimeter or if an illness indicative of the acquired immunodeficiency syndrome (i.e., an AIDS-defining illness) developed. The primary study end point was the diagnosis of genetically linked HIV-1 infection in the previously HIV-1-negative partner in an intention-to-treat analysis. Results Index participants were followed for 10,031 person-years; partners were followed for 8509 person-years. Among partners, 78 HIV-1 infections were observed during the trial (annual incidence, 0.9%; 95% confidence interval [CI], 0.7 to 1.1). Viral-linkage status was determined for 72 (92%) of the partner infections. Of these infections, 46 were linked (3 in the early-ART group and 43 in the delayed-ART group; incidence, 0.5%; 95% CI, 0.4 to 0.7) and 26 were unlinked (14 in the early-ART group and 12 in the delayed-ART group; incidence, 0.3%; 95% CI, 0.2 to 0.4). Early ART was associated with a 93% lower risk of linked partner infection than was delayed ART (hazard ratio, 0.07; 95% CI, 0.02 to 0.22). No linked infections were observed when HIV-1 infection was stably suppressed by ART in the index participant. Conclusions The early initiation of ART led to a sustained decrease in genetically linked HIV-1 infections in sexual partners. (Funded by the National Institute of Allergy and Infectious Diseases; HPTN 052 ClinicalTrials.gov number, NCT00074581). |
Global circulation patterns of seasonal influenza viruses vary with antigenic drift.
Bedford T , Riley S , Barr IG , Broor S , Chadha M , Cox NJ , Daniels RS , Gunasekaran CP , Hurt AC , Kelso A , Klimov A , Lewis NS , Li X , McCauley JW , Odagiri T , Potdar V , Rambaut A , Shu Y , Skepner E , Smith DJ , Suchard MA , Tashiro M , Wang D , Xu X , Lemey P , Russell CA . Nature 2015 523 (7559) 217-20 Understanding the spatiotemporal patterns of emergence and circulation of new human seasonal influenza virus variants is a key scientific and public health challenge. The global circulation patterns of influenza A/H3N2 viruses are well characterized, but the patterns of A/H1N1 and B viruses have remained largely unexplored. Here we show that the global circulation patterns of A/H1N1 (up to 2009), B/Victoria, and B/Yamagata viruses differ substantially from those of A/H3N2 viruses, on the basis of analyses of 9,604 haemagglutinin sequences of human seasonal influenza viruses from 2000 to 2012. Whereas genetic variants of A/H3N2 viruses did not persist locally between epidemics and were reseeded from East and Southeast Asia, genetic variants of A/H1N1 and B viruses persisted across several seasons and exhibited complex global dynamics with East and Southeast Asia playing a limited role in disseminating new variants. The less frequent global movement of influenza A/H1N1 and B viruses coincided with slower rates of antigenic evolution, lower ages of infection, and smaller, less frequent epidemics compared to A/H3N2 viruses. Detailed epidemic models support differences in age of infection, combined with the less frequent travel of children, as probable drivers of the differences in the patterns of global circulation, suggesting a complex interaction between virus evolution, epidemiology, and human behaviour. |
Assessment of the impact of rapid syphilis tests on syphilis screening and treatment of pregnant women in Zambia
Bonawitz RE , Duncan J , Hammond E , Hamomba L , Nambule J , Sambambi K , Musonda V , Calise A , Knapp A , Mwale J , McCauley J , Thea D , Herlihy JM . Int J Gynaecol Obstet 2015 130 Suppl 1 S58-62 OBJECTIVE: To evaluate the impact of rapid syphilis tests (RSTs) on syphilis testing and treatment in pregnant women in Kalomo District, Zambia. METHODS: In March 2012, health workers at all 35 health facilities in Kalomo Distract were trained in RST use and penicillin treatment. In March 2013, data were retrospectively abstracted from 18 randomly selected health facilities and stratified into three time intervals: baseline (6months prior to RST introduction), midline (0-6 months after RST introduction), and endline (7-12 months after RST introduction). RESULTS: Data collected on 4154 pregnant women showed a syphilis-reactive seroprevalence of 2.7%. The proportion of women screened improved from baseline (140/1365, 10.6%) to midline (976/1446, 67.5%), finally decreasing at endline (752/1337, 56.3%) (P<0.001). There was no significant difference in the proportion of syphilis-seroreactive pregnant women who received 1 dose of penicillin before (1/2, 50%) or after (5/48, 10.4%; P=0.199) RST introduction with low treatment rates throughout. CONCLUSION: With RST scale-up in Zambia and other resource-limited settings, same-day test and treatment with penicillin should be prioritized to achieve the goal of eliminating congenital syphilis. |
Declines in large wildlife increase landscape-level prevalence of rodent-borne disease in Africa
Young HS , Dirzo R , Helgen KM , McCauley DJ , Billeter SA , Kosoy MY , Osikowicz LM , Salkeld DJ , Young TP , Dittmar K . Proc Natl Acad Sci U S A 2014 111 (19) 7036-41 Populations of large wildlife are declining on local and global scales. The impacts of this pulse of size-selective defaunation include cascading changes to smaller animals, particularly rodents, and alteration of many ecosystem processes and services, potentially involving changes to prevalence and transmission of zoonotic disease. Understanding linkages between biodiversity loss and zoonotic disease is important for both public health and nature conservation programs, and has been a source of much recent scientific debate. In the case of rodent-borne zoonoses, there is strong conceptual support, but limited empirical evidence, for the hypothesis that defaunation, the loss of large wildlife, increases zoonotic disease risk by directly or indirectly releasing controls on rodent density. We tested this hypothesis by experimentally excluding large wildlife from a savanna ecosystem in East Africa, and examining changes in prevalence and abundance of Bartonella spp. infection in rodents and their flea vectors. We found no effect of wildlife removal on per capita prevalence of Bartonella infection in either rodents or fleas. However, because rodent and, consequently, flea abundance doubled following experimental defaunation, the density of infected hosts and infected fleas was roughly twofold higher in sites where large wildlife was absent. Thus, defaunation represents an elevated risk in Bartonella transmission to humans (bartonellosis). Our results (i) provide experimental evidence of large wildlife defaunation increasing landscape-level disease prevalence, (ii) highlight the importance of susceptible host regulation pathways and host/vector density responses in biodiversity-disease relationships, and (iii) suggest that rodent-borne disease responses to large wildlife loss may represent an important context where this relationship is largely negative. |
Effects of early versus delayed initiation of antiretroviral treatment on clinical outcomes of HIV-1 infection: results from the phase 3 HPTN 052 randomised controlled trial
Grinsztejn B , Hosseinipour MC , Ribaudo HJ , Swindells S , Eron J , Chen YQ , Wang L , Ou SS , Anderson M , McCauley M , Gamble T , Kumarasamy N , Hakim JG , Kumwenda J , Pilotto JH , Godbole SV , Chariyalertsak S , de Melo MG , Mayer KH , Eshleman SH , Piwowar-Manning E , Makhema J , Mills LA , Panchia R , Sanne I , Gallant J , Hoffman I , Taha TE , Nielsen-Saines K , Celentano D , Essex M , Havlir D , Cohen MS . Lancet Infect Dis 2014 14 (4) 281-90 BACKGROUND: Use of antiretroviral treatment for HIV-1 infection has decreased AIDS-related morbidity and mortality and prevents sexual transmission of HIV-1. However, the best time to initiate antiretroviral treatment to reduce progression of HIV-1 infection or non-AIDS clinical events is unknown. We reported previously that early antiretroviral treatment reduced HIV-1 transmission by 96%. We aimed to compare the effects of early and delayed initiation of antiretroviral treatment on clinical outcomes. METHODS: The HPTN 052 trial is a randomised controlled trial done at 13 sites in nine countries. We enrolled HIV-1-serodiscordant couples to the study and randomly allocated them to either early or delayed antiretroviral treatment by use of permuted block randomisation, stratified by site. Random assignment was unblinded. The HIV-1-infected member of every couple initiated antiretroviral treatment either on entry into the study (early treatment group) or after a decline in CD4 count or with onset of an AIDS-related illness (delayed treatment group). Primary events were AIDS clinical events (WHO stage 4 HIV-1 disease, tuberculosis, and severe bacterial infections) and the following serious medical conditions unrelated to AIDS: serious cardiovascular or vascular disease, serious liver disease, end-stage renal disease, new-onset diabetes mellitus, and non-AIDS malignant disease. Analysis was by intention-to-treat. This trial is registered with ClinicalTrials.gov, number NCT00074581. FINDINGS: 1763 people with HIV-1 infection and a serodiscordant partner were enrolled in the study; 886 were assigned early antiretroviral treatment and 877 to the delayed treatment group (two individuals were excluded from this group after randomisation). Median CD4 counts at randomisation were 442 (IQR 373-522) cells per muL in patients assigned to the early treatment group and 428 (357-522) cells per muL in those allocated delayed antiretroviral treatment. In the delayed group, antiretroviral treatment was initiated at a median CD4 count of 230 (IQR 197-249) cells per muL. Primary clinical events were reported in 57 individuals assigned to early treatment initiation versus 77 people allocated to delayed antiretroviral treatment (hazard ratio 0.73, 95% CI 0.52-1.03; p=0.074). New-onset AIDS events were recorded in 40 participants assigned to early antiretroviral treatment versus 61 allocated delayed initiation (0.64, 0.43-0.96; p=0.031), tuberculosis developed in 17 versus 34 patients, respectively (0.49, 0.28-0.89, p=0.018), and primary non-AIDS events were rare (12 in the early group vs nine with delayed treatment). In total, 498 primary and secondary outcomes occurred in the early treatment group (incidence 24.9 per 100 person-years, 95% CI 22.5-27.5) versus 585 in the delayed treatment group (29.2 per 100 person-years, 26.5-32.1; p=0.025). 26 people died, 11 who were allocated to early antiretroviral treatment and 15 who were assigned to the delayed treatment group. INTERPRETATION: Early initiation of antiretroviral treatment delayed the time to AIDS events and decreased the incidence of primary and secondary outcomes. The clinical benefits recorded, combined with the striking reduction in HIV-1 transmission risk previously reported, provides strong support for earlier initiation of antiretroviral treatment. FUNDING: US National Institute of Allergy and Infectious Diseases. |
Undisclosed antiretroviral drug use in a multinational clinical trial (HIV Prevention Trials Network 052)
Fogel JM , Wang L , Parsons TL , Ou SS , Piwowar-Manning E , Chen Y , Mudhune VO , Hosseinipour MC , Kumwenda J , Hakim JG , Chariyalertsak S , Panchia R , Sanne I , Kumarasamy N , Grinsztejn B , Makhema J , Pilotto J , Santos BR , Mayer KH , McCauley M , Gamble T , Bumpus NN , Hendrix CW , Cohen MS , Eshleman SH . J Infect Dis 2013 208 (10) 1624-8 The HIV Prevention Trials Network 052 study enrolled serodiscordant couples. Index participants infected with human immunodeficiency virus reported no prior antiretroviral (ARV) treatment at enrollment. ARV drug testing was performed retrospectively using enrollment samples from a subset of index participants. ARV drugs were detected in 45 of 96 participants (46.9%) with an undetectable viral load, 2 of 48 (4.2%) with a low viral load, and 1 of 65 (1.5%) with a high viral load (P < .0001); they were also detected in follow-up samples from participants who were not receiving study-administered treatment. ARV drug testing may be useful in addition to self-report of ARV drug use in some clinical trial settings. |
WHO recommendations for the viruses to be used in the 2012 Southern Hemisphere Influenza Vaccine: epidemiology, antigenic and genetic characteristics of influenza A(H1N1)pdm09, A(H3N2) and B influenza viruses collected from February to September 2011.
Klimov AI , Garten R , Russell C , Barr IG , Besselaar TG , Daniels R , Engelhardt OG , Grohmann G , Itamura S , Kelso A , McCauley J , Odagiri T , Smith D , Tashiro M , Xu X , Webby R , Wang D , Ye Z , Yuelong S , Zhang W , Cox N . Vaccine 2012 30 (45) 6461-71 In February and September each year the World Health Organisation (WHO) recommends influenza viruses to be included in influenza vaccines for the forthcoming winters in the Northern and Southern Hemispheres respectively. These recommendations are based on data collected by National Influenza Centres (NIC) through the Global Influenza Surveillance and Response System (GISRS) and a more detailed analysis of representative and potential antigenically variant influenza viruses from the WHO Collaborating Centres for Influenza (WHO CCs) and Essential Regulatory Laboratories (ERLs). This article provides a detailed summary of the antigenic and genetic properties of viruses and additional background data used by WHO experts during development of the recommendations for the 2012 Southern Hemisphere influenza vaccine composition. |
Exploring the choice to refuse or delay vaccines: a national survey of parents of 6- through 23-month-olds
McCauley MM , Kennedy A , Basket M , Sheedy K . Acad Pediatr 2012 12 (5) 375-83 OBJECTIVE: The purpose of this study was to assess respondents' self-reported choices for vaccinating their young children; knowledge, attitudes, and beliefs (KABs) about vaccination; and communication with their child's vaccination provider. METHODS: A national telephone survey of 1500 parents of children aged 6 to 23 months was conducted in 2010. We calculated proportions of parents who had chosen-or planned-to refuse or delay 1 or more recommended vaccines, and proportions for responses to KABs and communication questions, stratified by vaccination choice (ie, refuse or delay). RESULTS: The response rate was 46%. Among the 96.6% of respondents (95% confidence interval [CI], 95.5%-97.4%; weighted n = 1453) who had chosen for their child to receive at least 1 vaccine, 80.6% (95% CI, 78.8%-83.0%) reported that their child had received all vaccines when recommended and 86.5% (95% CI, 84.7%-88.2%) reported that their child would receive remaining vaccines when recommended. Respondents who considered not following recommendations, but ultimately did, cited the physician's recommendation as the reason for vaccinating. Most vaccinators who reported past or planned deviations from recommendations cited only 1 vaccine that they would refuse and/or delay; all vaccines were mentioned. These parents reported approaching vaccination with serious concerns, while believing other parents did not. All parents cited "vaccine side effects" as their top question or concern. Almost all parents talked to a doctor or nurse about vaccines and, overall, satisfaction with communication was high. CONCLUSIONS: Communication about vaccines is important to most parents, but may be challenging for providers, because parental choices vary; thus, efforts to improve and support vaccine communication by providers should continue. |
Racial inequities in receipt of influenza vaccination among nursing home residents in the United States, 2008-2009: a pattern of low overall coverage in facilities in which most residents are black
Bardenheier B , Wortley P , Shefer A , McCauley MM , Gravenstein S . J Am Med Dir Assoc 2012 13 (5) 470-6 OBJECTIVES: Nationwide among nursing home residents, receipt of the influenza vaccine is 8 to 9 percentage points lower among blacks than among whites. The objective of this study was to determine if the national inequity in vaccination is because of the characteristics of facilities and/or residents. DESIGN: Cross-sectional study with multilevel modeling. SETTING AND PARTICIPANTS: States in which 1% or more of nursing home residents were black and the difference in influenza vaccination coverage between white and black nursing home residents was 1 percentage point or higher (n = 39 states and the District of Columbia). Data on residents (n = 2,359,321) were obtained from the Centers for Medicare & Medicaid Service's Minimum Data Set for October 1, 2008, through March 31, 2009. MEASUREMENTS: Residents' influenza vaccination status (vaccinated, refused vaccine, or not offered vaccination). RESULTS: States with higher overall influenza vaccination coverage among nursing home residents had smaller racial inequities. In nursing homes with higher proportions of black residents, vaccination coverage was lower for both blacks and whites. The most dramatic inequities existed between whites in nursing homes with 0% blacks (L1) and blacks in nursing homes with 50% or more blacks (L5) in states with overall racial inequities of 10 percentage points or more. In these states, more black nursing home residents lived in nursing homes with 50% or more blacks (L5); in general, the same homes with low overall coverage. CONCLUSION: Inequities in influenza vaccination coverage among nursing home residents are largely because of low vaccination coverage in nursing homes with a high proportion of black residents. Findings indicate that implementation of culturally appropriate interventions to increase vaccination in facilities with larger proportions of black residents may reduce the racial gap in influenza vaccination as well as increase overall state-level vaccination. |
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