Last data update: May 13, 2024. (Total: 46773 publications since 2009)
Records 1-29 (of 29 Records) |
Query Trace: Parrish A[original query] |
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Understanding the divergent evolution andepidemiology of H3N8 influenza viruses indogs andhorses
Wasik BR , Rothschild E , Voorhees IEH , Reedy SE , Murcia PR , Pusterla N , Chambers TM , Goodman LB , Holmes EC , Kile JC , Parrish CR . Virus Evol 2023 9 (2) vead052 Cross-species virus transmission events can lead to dire public health emergencies in the form of epidemics and pandemics. One example in animals is the emergence of the H3N8 equine influenza virus (EIV), first isolated in 1963 in Miami, FL, USA, after emerging among horses in South America. In the early 21st century, the American lineage of EIV diverged into two 'Florida' clades that persist today, while an EIV transferred to dogs around 1999 and gave rise to the H3N8 canine influenza virus (CIV), first reported in 2004. Here, we compare CIV in dogs and EIV in horses to reveal their host-specific evolution, to determine the sources and connections between significant outbreaks, and to gain insight into the factors controlling their different evolutionary fates. H3N8 CIV only circulated in North America, was geographically restricted after the first few years, and went extinct in 2016. Of the two EIV Florida clades, clade 1 circulates widely and shows frequent transfers between the USA and South America, Europe and elsewhere, while clade 2 was globally distributed early after it emerged, but since about 2018 has only been detected in Central Asia. Any potential zoonotic threat of these viruses to humans can only be determined with an understanding of its natural history and evolution. Our comparative analysis of these three viral lineages reveals distinct patterns and rates of sequence variation yet with similar overall evolution between clades, suggesting epidemiological intervention strategies for possible eradication of H3N8 EIV. |
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. |
Understanding the Divergent Evolution and Epidemiology of H3N8 Influenza Viruses in Dogs and Horses (preprint)
Wasik BR , Rothschild E , Voorhees IEH , Reedy SE , Murcia PR , Pusterla N , Chambers TM , Goodman LB , Holmes EC , Kile JC , Parrish CR . bioRxiv 2023 23 Cross-species virus transmission events can lead to dire public health emergencies in the form of epidemics and pandemics. One example in animals is the emergence of the H3N8 equine influenza virus (EIV), first isolated in 1963 in Miami, Florida after emerging among horses in South America. In the early 21st century the American lineage of EIV diverged into two 'Florida' clades that persist today, while an EIV transferred to dogs around 1999 and gave rise to the H3N8 canine influenza virus (CIV), first reported in 2004. Here, we compare CIV in dogs and EIV in horses to clarify their host-specific evolution, to determine the sources and connections between significant outbreaks, and to gain insight into the factors controlling their different evolutionary fates. H3N8 CIV only circulated in North America, was geographically restricted after the first few years, and went extinct in 2016. Of the two EIV Florida clades, clade 1 circulates widely and shows frequent transfers between the USA and South America, Europe and elsewhere, while clade 2 was globally distributed early after it emerged, but since about 2018 has only been detected in Central Asia. Any potential zoonotic threat of these viruses to humans can only be determined with an understanding of its natural history and evolution. Our comparative analysis of these three viral lineages reveals both distinct patterns and rates of sequence variation yet with similar overall evolution between clades, suggesting epidemiological intervention strategies for possible eradication of H3N8 EIV. (242 words) Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license. |
Replication and validation of a state-wide linkage method to estimate incidence proportion of child maltreatment
Newby-Kew A , Marshall LM , Zane S , Putz JW , Parrish J . Ann Epidemiol 2023 84 1-7 PURPOSE: To study familial factors associated with child maltreatment in a birth population, Alaska piloted a mixed-design method that linked child welfare data with the Pregnancy Risk Assessment Monitoring System (PRAMS). We replicated this approach in Oregon and validated it in both states. METHODS: We linked vital records, child welfare, and PRAMS data to create two 2009 birth cohorts for each state: one based on vital records (full birth cohort), and one on PRAMS (stratified random sample). For each cohort we estimated the incidence proportions (IP) of child maltreatment before age nine years and compared those estimated using PRAMS with those observed using the full birth cohort. RESULTS: The Oregon PRAMS cohort estimated that 28.7% (95% CI: 24.0, 33.4), 20.9% (17.1, 24.7), and 8.3% (6.0, 10.5) of children experienced an alleged, investigated, and substantiated maltreatment respectively, versus 32.0%, 25.0% and 9.9% from the birth cohort. The corresponding Alaska estimates were 29.1% (26.1, 32.0), 22.6% (19.9, 25.2), and 8.3% (6.7, 9.9) of children from the PRAMS cohort versus 29.1%, 23.5%, and 9.1% in the birth cohort. CONCLUSIONS: The incidence proportion of child maltreatment in two states was accurately estimated with PRAMS cohorts. Researchers can study a comprehensive set of factors that may influence child maltreatment by incorporating PRAMS into birth cohort linkages. |
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. |
A sub-group evaluation of the multi-month dispensing strategy for differentiated HIV care: is personalization of care guidelines warranted in Haiti
Parrish C , Basu A , Fishman P , Koama JB , Robin E , Francois K , Honoré JG , Van Onacker JD , Puttkammer N . BMC Health Serv Res 2022 22 (1) 80 BACKGROUND: Differentiated care strategies are rapidly becoming the norm for HIV care delivery globally. Building upon an interest in tailoring antiretroviral therapy (ART) delivery for client-centered needs, the Ministry of Health and Population in Haiti formally endorsed multiple-month dispenses (MMD) in the 2016 national ART guidelines This study explores heterogeneity in retention in care with MMD for specific Haitian populations living with HIV and evaluates if a targeted algorithm for optimal ART prescription intervals is warranted in Haiti. METHODS: This study included ART-naïve individuals who started ART on or after January 1st, 2017 in Haiti. To identify subgroups in which to explore heterogeneity of retention, we implemented a double-lasso regression method to determine which individual characteristics would define the subgroups. Characteristics evaluated for potential subgroup definition included: sex, age category, WHO clinical stage, and body mass index category. We employed instrumental variable models to estimate the causal effect of increasing ART dispensing length on ART retention, by client subgroup. The outcome of interest was retention in care after one year in treatment. We then estimated the marginal effect of a 30-day increase to ART dispensing length to retention in care for each of these subgroups. RESULTS: There was evidence for heterogeneity in the effect of extending ART dispensing intervals on retention by WHO clinical stage. We observed significant improvements to retention in care at one year with a 30-day increase in ART dispense length for all subgroups defined by WHO clinical stages 1-4. The effects ranged from a 14.7% increase (95% CI: 12.4-17.0) to the likelihood of retention for people with HIV in WHO stage 1 to a 21.6% increase (95% CI: 18.7-24.5) to the likelihood of retention for those in WHO stage 3. CONCLUSIONS: All the subgroups defined by WHO clinical stage experienced a benefit of extending ART intervals to retention in care at one year. Though the effect did differ slightly by WHO stage, the effects went in the same direction and were of similar magnitude. Therefore, a standardized recommendation for MMD among those living with HIV and new on ART is appropriate for Haiti treatment guidelines. |
Timely initiation of HIV antiretroviral therapy in Haiti 2004-2018: a retrospective cohort study
Puttkammer N , Parrish C , Desir Y , Hyppolite N , Joseph N , Hall L , Honoré JG , Robin E , Perrin G , François K . Rev Panam Salud Publica 2021 45 e139 OBJECTIVE: To describe trends in timing of ART initiation for newly diagnosed people living with HIV before and after Haiti adopted its Test and Start policy for universal HIV antiretroviral therapy (ART) in July 2016, and to explore predictors of timely ART initiation for both newly and previously diagnosed people living with HIV following Test and Start adoption. METHODS: This retrospective cohort study explored timing of ART initiation among 147 900 patients diagnosed with HIV at 94 ART clinics in 2004-2018 using secondary electronic medical record data. The study used survival analysis methods to assess time trends and risk factors for ART initiation. RESULTS: Timely uptake of ART expanded with Test and Start, such that same-day ART initiation rates increased from 3.7% to 45.0%. However, only 11.0% of previously diagnosed patients initiated ART after Test and Start. In adjusted analyses among newly diagnosed people living with HIV, factors negatively associated with timely ART initiation included being a pediatric patient aged 0-14 years (HR = 0.23, p < 0.001), being male (HR = 0.92, p = 0.03), being 50+ years (HR = 0.87, p = 0.03), being underweight (HR = 0.79, p < 0.001), and having WHO stage 3 (HR = 0.73, p < 0.001) or stage 4 disease (HR = 0.49, p < 0.001). Variation in timely ART initiation by geographic department and health facility was observed. CONCLUSIONS: Haiti has made substantial progress in scaling up Test and Start, but further work is needed to enroll previously diagnosed patients and to ensure rapid ART in key patient subgroups. Further research is needed on facility and geographic factors and on strategies for improving timely ART initiation among vulnerable subgroups. |
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. |
Estimating the effect of increasing dispensing intervals on retention in care for people with HIV in Haiti
Parrish C , Basu A , Fishman P , Koama JB , Robin E , Francois K , Honore JG , Van Onacker JD , Puttkammer N . EClinicalMedicine 2021 38 101039 Background: Multi-month dispensing (MMD) for antiretroviral therapy (ART) is a promising care strategy to improve HIV treatment adherence. The effectiveness of MMD in routine settings has not yet been evaluated within a causal inference framework. We analyzed data from a robust clinical data system to evaluate MMD in Haiti. Method(s): We assessed 1-year retention in care among 21,880 ART-naive HIV-positive persons who started ART on or after January 1, 2017, up until November 1, 2018. We used an instrumental variable analysis to estimate the causal impact of MMD. This approach was used to address potential selection into specific dispensing intervals because MMD is not randomly applied to individuals. Finding(s): We found that extending ART dispensing intervals increased the probability of retention at 12 months after ART initiation, with up to a 24.2%-point increase (95%CI: 21.9, 26.5) in the likelihood of retention with extending dispenses by 30 days for those receiving one-month dispenses. We observed statistically significant gains to retention with MMD with up to an approximately 4-month supply of ART; +5.1%-points (95%CI: 2.4,7.8). Increasing dispensing lengths for those already receiving >=5-month supply of ART had a potentially negative effect on retention. Interpretation(s): MMD for ART is an effective service delivery strategy that improves care retention for new ART recipients. There is a potentially negative effect of increasing prescription lengths for those new ART recipients already receiving longer ART supplies, though more research is needed to characterize this effect given medication supplies of this length are not common for newer ART recipients. Copyright © 2021 The Author(s) |
Primary Swine Respiratory Epithelial Cell Lines for the Efficient Isolation and Propagation of Influenza A Viruses.
Meliopoulos V , Cherry S , Wohlgemuth N , Honce R , Barnard K , Gauger P , Davis T , Shult P , Parrish C , Schultz-Cherry S . J Virol 2020 94 (24) Influenza virus isolation from clinical samples is critical for the identification and characterization of circulating and emerging viruses. Yet efficient isolation can be difficult. In these studies, we isolated primary swine nasal and tracheal respiratory epithelial cells and immortalized swine nasal epithelial cells (siNEC) and tracheal epithelial cells (siTEC) that retained the abilities to form tight junctions and cilia and to differentiate at the air-liquid interface like primary cells. Critically, both human and swine influenza viruses replicated in the immortalized cells, which generally yielded higher-titer viral isolates from human and swine nasal swabs, supported the replication of isolates that failed to grow in Madin-Darby canine kidney (MDCK) cells, and resulted in fewer dominating mutations during viral passaging than MDCK cells.IMPORTANCE Robust in vitro culture systems for influenza virus are critically needed. MDCK cells, the most widely used cell line for influenza isolation and propagation, do not adequately model the respiratory tract. Therefore, many clinical isolates, both animal and human, are unable to be isolated and characterized, limiting our understanding of currently circulating influenza viruses. We have developed immortalized swine respiratory epithelial cells that retain the ability to differentiate and can support influenza replication and isolation. These cell lines can be used as additional tools to enhance influenza research and vaccine development. |
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. |
Toward universal HIV treatment in Haiti: Time trends in ART retention following expanded ART eligibility in a national cohort from 2011-17
Puttkammer N , Parrish C , Desir Y , Hyppolite N , Wagenaar B , Joseph N , Hall L , Honore JG , Robin E , Perrin G , Francois K . J Acquir Immune Defic Syndr 2020 84 (2) 153-161 BACKGROUND: The World Health Organization (WHO) recommends universal antiretroviral therapy (ART) for people living with HIV (PLWH), but evidence about effects of expanded ART access on ART retention in low-resource settings is limited. SETTING: Haiti's Ministry of Health endorsed universal ART for pregnant women in March 2013 (Option B+) and for all PLWH in July 2016. This study included 51,579 ART patients from 2011-17 at 94 hospitals and clinics in Haiti. METHODS: This observational, retrospective cohort study described time trends in 6-month ART retention using secondary data, and compared results during three time periods using an interrupted time series (ITS) model: pre-Option B+ (period 1: 1/11-2/13), Option B+ (period 2: 3/13-6/16), and Test and Start (T&S, period 3: 7/16-9/17). RESULTS: From the pre-Option B+ to the T&S period, the monthly count of new ART patients increased from 366/month to 877/month, and the proportion with same-day ART increased from 6.3% to 42.1% (p<0.001). The proportion retained on ART after 6 months declined from 78.4% to 75.0% (p<0.001). In the ITS model, ART retention improved by a rate of 1.4% per quarter during the T&S period after adjusting for patient characteristics (Adjusted Incidence Rate Ratio [aIRR]=1.014; 95% confidence interval [CI]: 1.002-1.026, p<0.001). However, patients with same-day ART were 14% less likely to be retained compared to those starting ART >30 days after HIV diagnosis (aIRR=0.86; 95% CI: 0.84-0.89, p<0.001). CONCLUSION: Achieving targets for HIV epidemic control will require increasing ART retention and reducing the disparity in retention for those with same-day ART. |
Male mortality trends in the United States, 1900-2010: Progress, challenges, and opportunities
Jones WK , Hahn RA , Parrish RG , Teutsch SM , Chang MH . Public Health Rep 2019 135 (1) 33354919893029 OBJECTIVES: Male mortality fell substantially during the past century, and major causes of death changed. Building on our recent analysis of female mortality trends in the United States, we examined all-cause and cause-specific mortality trends at each decade from 1900 to 2010 among US males. METHODS: We conducted a descriptive study of age-adjusted death rates (AADRs) for 11 categories of disease and injury stratified by race (white, nonwhite, and, when available, black), the excess of male mortality over female mortality ([male AADR - female AADR]/female AADR), and potential causes of persistent excess of male mortality. We used national mortality data for each decade. RESULTS: From 1900 to 2010, the all-cause AADR declined 66.4% among white males and 74.5% among nonwhite males. Five major causes of death in 1900 were pneumonia and influenza, heart disease, stroke, tuberculosis, and unintentional nonmotor vehicle injuries; in 2010, infectious conditions were replaced by cancers and chronic lower respiratory diseases. The all-cause excess of male mortality rose from 9.1% in 1900 to 65.5% in 1980 among white males and a peak of 63.7% in 1990 among nonwhite males, subsequently falling among all groups. CONCLUSION: During the last century, AADRs among males declined more slowly than among females. Although the gap diminished in recent decades, exploration of social and behavioral factors may inform interventions that could further reduce death rates among males. |
Risk factors for oral HPV infection among young men who have sex with men - 2 cities, United States, 2012-2014
Oliver SE , Gorbach P , Gratzer B , Steinau M , Collins T , Parrish A , Kerndt PR , Crosby R , Unger ER , Markowitz LE , Meites E . Sex Transm Dis 2018 45 (10) 660-665 BACKGROUND: Men who have sex with men (MSM) are at risk for cancers attributable to human papillomavirus (HPV), including oropharyngeal cancer. HPV vaccination is recommended for U.S. MSM through age 26 years. Oral HPV infection is associated with oropharyngeal cancer. We determined oral HPV prevalence and risk factors among young MSM. METHODS: The Young Men's HPV study enrolled MSM aged 18-26 years from clinics in Chicago and Los Angeles during 2012-2014. Participants self-reported demographics, sexual behaviors, vaccination and HIV status. Self-collected oral rinse specimens were tested for HPV DNA (37 types) by L1-consensus PCR. We calculated adjusted prevalence ratios (aPR) and 95% confidence intervals (CI) for risk factors associated with oral HPV among participants not previously vaccinated. RESULTS: Oral HPV was detected in 87/922 (9.4%); 9-valent vaccine (9vHPV) types were detected in 37/922 (4.0%). Among HIV-positive participants, 17/88 (19.3%) had oral HPV detected. Oral HPV was more prevalent among those reporting first sex at age </=18 years (aPR:2.44; CI:1.16-5.12); HIV infection (aPR:1.99; CI:1.14-3.48); >5 sex partners within the past month (aPR:1.93; CI:1.13-3.31); performing oral sex on >5 partners within the last 3 months (aPR:1.87; CI:1.12-3.13); and having >5 male sex partners within the last 3 months (aPR:1.76; CI: 1.08-2.87). Only 454/922 (49.2%) were aware HPV can cause oropharyngeal cancers. CONCLUSIONS: Many oral HPV infections were with types targeted by vaccination. Oral HPV infections were significantly associated with HIV and sexual behaviors. Fewer than half of participants were aware HPV could cause oropharyngeal cancer. |
Risk factors for oral HPV infection among young men who have sex with men - 2 cities, United States, 2012-2014
Oliver SE , Gorbach P , Gratzer B , Steinau M , Collins T , Parrish A , Kerndt PR , Crosby R , Unger ER , Markowitz LE , Meites E . Sex Transm Dis 2018 45 (10) 660-665 BACKGROUND: Men who have sex with men (MSM) are at risk for cancers attributable to human papillomavirus (HPV), including oropharyngeal cancer. HPV vaccination is recommended for U.S. MSM through age 26 years. Oral HPV infection is associated with oropharyngeal cancer. We determined oral HPV prevalence and risk factors among young MSM. METHODS: The Young Men's HPV study enrolled MSM aged 18-26 years from clinics in Chicago and Los Angeles during 2012-2014. Participants self-reported demographics, sexual behaviors, vaccination and HIV status. Self-collected oral rinse specimens were tested for HPV DNA (37 types) by L1-consensus PCR. We calculated adjusted prevalence ratios (aPR) and 95% confidence intervals (CI) for risk factors associated with oral HPV among participants not previously vaccinated. RESULTS: Oral HPV was detected in 87/922 (9.4%); 9-valent vaccine (9vHPV) types were detected in 37/922 (4.0%). Among HIV-positive participants, 17/88 (19.3%) had oral HPV detected. Oral HPV was more prevalent among those reporting first sex at age </=18 years (aPR:2.44; CI:1.16-5.12); HIV infection (aPR:1.99; CI:1.14-3.48); >5 sex partners within the past month (aPR:1.93; CI:1.13-3.31); performing oral sex on >5 partners within the last 3 months (aPR:1.87; CI:1.12-3.13); and having >5 male sex partners within the last 3 months (aPR:1.76; CI: 1.08-2.87). Only 454/922 (49.2%) were aware HPV can cause oropharyngeal cancers. CONCLUSIONS: Many oral HPV infections were with types targeted by vaccination. Oral HPV infections were significantly associated with HIV and sexual behaviors. Fewer than half of participants were aware HPV could cause oropharyngeal cancer. |
A review of global literature on using administrative data to estimate prevalence of intellectual and developmental disabilities
Friedman DJ , Gibson Parrish R , Fox MH . J Policy Pract Intellect Disabil 2018 15 (1) 43-62 As understanding of health deficits among people with intellectual and developmental disabilities (IDD) increases, concerns grow about how to develop comprehensive, sustainable surveillance systems to reliably monitor the health of this population over time. This study reviews literature from 12 countries in which retrospective administrative data have been used to estimate population-based prevalence of IDD, identifies promising practices in that literature, and discusses the feasibility of applying those promising practices to other countries. Administrative data sources can be used to identify the number of people with IDD (numerators) in the presence of population estimates from which people with IDD are drawn (denominators) for discrete geographic locations. Case ascertainment methods, age groupings, data years captured, and other methods vary, contributing to a wide variation in prevalence rates. Six methods are identified from five countries that appear to offer the greatest likelihood of expanded applications. Approaches in which administrative data collections are linked with other population-based data sources appear promising as a means of estimating the size and characteristics of populations living with IDD in defined geographic locations. They offer the potential for sustainability, timeliness, accuracy, and efficiency. |
Trends in mortality among females in the United States, 1900-2010: Progress and challenges
Hahn RA , Chang MH , Parrish RG , Teutsch SM , Jones WK . Prev Chronic Dis 2018 15 E30 INTRODUCTION: We analyzed trends in US female mortality rates by decade from 1900 through 2010, assessed age and racial differences, and proposed explanations and considered implications. METHODS: We conducted a descriptive study of trends in mortality rates from major causes of death for females in the United States from 1900 through 2010. We analyzed all-cause unadjusted death rates (UDRs) for males and females and for white and nonwhite males and females from 1900 through 2010. Data for blacks, distinct from other nonwhites, were available beginning in 1970 and are reported for this and following decades. We also computed age-adjusted all-cause death rates (AADRs) by the direct method using age-specific death rates and the 2000 US standard population. Data for the analysis of decadal trends in mortality rates were obtained from yearly tabulations of causes of death from published compilations and from public use computer data files. RESULTS: In 1900, UDRs and AADRs were higher for nonwhites than whites and decreased more rapidly for nonwhite females than for white females. Reductions were highest among younger females and lowest among older females. Rates for infectious diseases decreased the most. AADRs for heart disease increased 96.5% in the first 5 decades, then declined by 70.6%. AADRs for cancer rose, then decreased. Stroke decreased steadily. Unintentional motor vehicle injury AADRs increased, leveled off, then decreased. Differences between white and nonwhite female all-cause AADRs almost disappeared during the study period (5.4 per 100,000); differences in white and black AADRs remained high (121.7 per 100,000). CONCLUSION: Improvements in social and environmental determinants of health probably account for decreased mortality rates among females in the early 20th century, partially offset by increased smoking. In the second half of the century, other public health and clinical measures contributed to reductions. The persistent prevalence of risk behaviors and underuse of preventive and medical services indicate opportunities for increased female longevity, particularly in racial minority populations. |
Using reduced inoculum densities of Mycobacterium tuberculosis in MGIT Pyrazinamide Susceptibility Testing to prevent false-resistant results and improve accuracy: A multicenter evaluation
Morlock GP , Tyrrell FC , Baynham D , Escuyer VE , Green N , Kim Y , Longley-Olson PA , Parrish N , Pennington C , Tan D , Austin B , Posey JE . Tuberc Res Treat 2017 2017 3748163 The primary platform used for pyrazinamide (PZA) susceptibility testing of Mycobacterium tuberculosis is the MGIT culture system (Becton Dickinson). Since false-resistant results have been associated with the use of this system, we conducted a multicenter evaluation to determine the effect of using a reduced cell density inoculum on the rate of false resistance. Two reduced inoculum densities were compared with that prescribed by the manufacturer (designated as "BD" method). The reduced inoculum methods (designated as "A" and "C") were identical to the manufacturer's protocol in all aspects with the exception of the cell density of the inoculum. Twenty genetically and phenotypically characterized M. tuberculosis isolates were tested in duplicate by ten independent laboratories using the three inoculum methods. False-resistant results declined from 21.1% using the standard "BD" method to 5.7% using the intermediate ("A") inoculum and further declined to 2.8% using the most dilute ("C") inoculum method. The percentages of the resistant results that were false-resistant declined from 55.2% for the "BD" test to 28.8% and 16.0% for the "A" and "C" tests, respectively. These results represent compelling evidence that the occurrence of false-resistant MGIT PZA susceptibility test results can be mitigated through the use of reduced inoculum densities. |
Human papillomavirus vaccination among young men who have sex with men and transgender women in 2 US cities, 2012-2014
Gorbach PM , Cook R , Gratzer B , Collins T , Parrish A , Moore J , Kerndt PR , Crosby RA , Markowitz LE , Meites E . Sex Transm Dis 2017 44 (7) 436-441 BACKGROUND: Since 2011, in the United States, quadrivalent human papillomavirus (HPV) vaccine has been recommended for boys aged 11 to 12 years, men through age 21, and men who have sex with men (MSM) through age 26. We assessed HPV vaccination coverage and factors associated with vaccination among young MSM (YMSM) and transgender women (TGW) in 2 cities. METHODS: During 2012-2014, 808 YMSM and TGW aged 18 to 26 years reported vaccination status in a self-administered computerized questionnaire at 3 sexually transmitted disease (STD) clinics in Los Angeles and Chicago. Associations with HPV vaccination were assessed using bivariate and multivariable models to calculate adjusted odds ratios (aORs) and 95% confidence intervals (CIs). RESULTS: Few of the diverse participants (Hispanic/Latino, 38.0%; white, 27.0%; and black/African American, 17.9%) reported receiving 1 or more HPV vaccine doses (n = 111 [13.7%]) and even fewer reported 3 doses (n = 37 [4.6%]). A multivariable model found associations between vaccination and having a 4-year college degree or higher (aOR, 2.83; CI, 1.55-5.17) and self-reported STDs (aOR, 1.21; CI, 1.03-1.42). In a model including recommendation variables, the strongest predictor of vaccination was a health care provider recommendation (aOR, 11.85; CI, 6.70-20.98). CONCLUSIONS: Human papillomavirus vaccination coverage was low among YMSM and TGW in this 2-US city study. Our findings suggest further efforts are needed to reach YMSM seeking care in STD clinics, increase strong recommendations from health care providers, and integrate HPV vaccination with other clinical services such as STD testing. |
Preventing alcohol and tobacco exposed pregnancies: CHOICES Plus in primary care
Velasquez MM , von Sternberg KL , Floyd RL , Parrish D , Kowalchuk A , Stephens NS , Ostermeyer B , Green C , Seale JP , Mullen PD . Am J Prev Med 2017 53 (1) 85-95 INTRODUCTION: Alcohol and tobacco use are common among U.S. women, yet if used during pregnancy these substances present significant preventable risks to prenatal and perinatal health. Because use of alcohol and tobacco often continue into the first trimester and beyond, especially among women with unintended pregnancies, effective evidence-based approaches are needed to decrease these risk behaviors. This study was designed to test the efficacy of CHOICES Plus, a preconception intervention for reducing the risk of alcohol- and tobacco-exposed pregnancies (AEPs and TEPs). STUDY DESIGN: RCT with two intervention groups: CHOICES Plus (n=131) versus Brief Advice (n=130). Data collected April 2011 to October 2013. Data analysis finalized February 2016. SETTING/PARTICIPANTS: Settings were 12 primary care clinics in a large Texas public healthcare system. Participants were women who were non-sterile, non-pregnant, aged 18-44 years, drinking more than three drinks per day or more than seven drinks per week, sexually active, and not using effective contraception (N=261). Forty-five percent were smokers. INTERVENTION: Interventions were two CHOICES Plus sessions and a contraceptive visit or Brief Advice and referral to community resources. MAIN OUTCOME MEASURES: Primary outcomes were reduced risk of AEP and TEP through 9-month follow-up. RESULTS: In intention-to-treat analyses across 9 months, the CHOICES Plus group was more likely than the Brief Advice group to reduce risk of AEP with an incidence rate ratio of 0.620 (95% CI=0.511, 0.757) and absolute risk reduction of -0.233 (95% CI= -0.239, -0.226). CHOICES Plus group members at risk for both exposures were more likely to reduce TEP risk (incidence rate ratio, 0.597; 95% CI=0.424, 0.840 and absolute risk reduction, -0.233; 95% CI= -0.019, -0.521). CONCLUSIONS: CHOICES Plus significantly reduced AEP and TEP risk. Addressing these commonly co-occurring risk factors in a single preconception program proved both feasible and efficacious in a low-income primary care population. Intervening with women before they become pregnant could shift the focus in clinical practice from treatment of substance-exposed pregnancies to prevention of a costly public health concern. TRIAL REGISTRATION: This study is registered at clinicaltrials.gov NCT01032772. |
Promoting influenza vaccination to restaurant employees
Graves MC , Harris JR , Hannon PA , Hammerback K , Parrish AT , Ahmed F , Zhou C , Allen CL . Am J Health Promot 2016 30 (7) 498-500 PURPOSE: To evaluate an evidence-based workplace approach to increasing adult influenza vaccination levels applied in the restaurant setting DESIGN: We implemented an intervention and conducted a pre/post analysis to determine effect on vaccination. SETTING: Eleven Seattle-area restaurants. SUBJECTS: Restaurants with 25+ employees speaking English or Spanish and over 18 years. INTERVENTION: Restaurants received influenza vaccination promotion materials, assistance arranging on-site vaccination events, and free influenza vaccinations for employees. MEASURES: Pre/post employee surveys of vaccination status with direct observation and employer interviews to evaluate implementation. ANALYSIS: We conducted descriptive analysis of employee survey data and performed qualitative analysis of implementation data. To assess intervention effect, we used a mixed-effects logistic regression model with a restaurant-specific random effect. RESULTS: Vaccination levels increased from 26% to 46% (adjusted odds ratio 2.33, 95% confidence interval 1.69, 3.22), with 428 employees surveyed preintervention, 305 surveyed postintervention, and response rates of 73% and 55%, respectively. The intervention was effective across subgroups, but there were restaurant-level differences. CONCLUSION: An access-based workplace intervention can increase influenza vaccination levels in restaurant employees, but restaurant-level factors may influence success. |
Monitoring for Human Papillomavirus Vaccine Impact Among Gay, Bisexual, and Other Men Who Have Sex With Men-United States, 2012-2014
Meites E , Gorbach PM , Gratzer B , Panicker G , Steinau M , Collins T , Parrish A , Randel C , McGrath M , Carrasco S , Moore J , Zaidi A , Braxton J , Kerndt PR , Unger ER , Crosby RA , Markowitz LE . J Infect Dis 2016 BACKGROUND: Gay, bisexual, and other men who have sex with men (MSM) are at high risk for HPV; vaccination is recommended for U.S. males, including MSM through age 26. We assessed evidence of HPV among vaccine-eligible MSM and transgender women to monitor vaccine impact. METHODS: During 2012-14, MSM age 18-26 at selected clinics completed a computer-assisted self-interview regarding sexual behavior, HIV status, and vaccinations. Self-collected anal swab and oral rinse specimens were tested for HPV DNA (37 types) by L1 consensus PCR; serum was tested for HPV antibodies (4 types) by multiplexed VLP-based IgG direct ELISA. RESULTS: Among 922 vaccine-eligible participants, mean age was 23, and mean number of lifetime sex partners was 37. Among 834 without HIV, any anal HPV was detected in 69.4% and any oral HPV in 8.4%, yet only 8.5% had evidence of exposure to all quadrivalent vaccine types. In multivariate analysis, HPV prevalence varied significantly (p<0.05) by HIV status, sexual orientation, and lifetime sex partners, but not race/ethnicity. DISCUSSION: Most young MSM lacked evidence of current or past infection with all vaccine-type HPV, suggesting they could benefit from vaccination. Vaccination impact among MSM may be assessed by monitoring HPV prevalence, including in self-collected specimens. |
Adverse drug reactions causing admission to medical wards: A cross-sectional survey at 4 hospitals in South Africa
Mouton JP , Njuguna C , Kramer N , Stewart A , Mehta U , Blockman M , Fortuin-De Smidt M , De Waal R , Parrish AG , Wilson DP , Igumbor EU , Aynalem G , Dheda M , Maartens G , Cohen K . Medicine (Baltimore) 2016 95 (19) e3437 Limited data exist on the burden of serious adverse drug reactions (ADRs) in sub-Saharan Africa, which has high HIV and tuberculosis prevalence. We determined the proportion of adult admissions attributable to ADRs at 4 hospitals in South Africa. We characterized drugs implicated in, risk factors for, and the preventability of ADR-related admissions.We prospectively followed patients admitted to 4 hospitals' medical wards over sequential 30-day periods in 2013 and identified suspected ADRs with the aid of a trigger tool. A multidisciplinary team performed causality, preventability, and severity assessment using published criteria. We categorized an admission as ADR-related if the ADR was the primary reason for admission.There were 1951 admissions involving 1904 patients: median age was 50 years (interquartile range 34-65), 1057 of 1904 (56%) were female, 559 of 1904 (29%) were HIV-infected, and 183 of 1904 (10%) were on antituberculosis therapy (ATT). There were 164 of 1951 (8.4%) ADR-related admissions. After adjustment for age and ATT, ADR-related admission was independently associated (P ≤ 0.02) with female sex (adjusted odds ratio [aOR] 1.51, 95% confidence interval [95% CI] 1.06-2.14), increasing drug count (aOR 1.14 per additional drug, 95% CI 1.09-1.20), increasing comorbidity score (aOR 1.23 per additional point, 95% CI 1.07-1.41), and use of antiretroviral therapy (ART) if HIV-infected (aOR 1.92 compared with HIV-negative/unknown, 95% CI 1.17-3.14). The most common ADRs were renal impairment, hypoglycemia, liver injury, and hemorrhage. Tenofovir disoproxil fumarate, insulin, rifampicin, and warfarin were most commonly implicated, respectively, in these 4 ADRs. ART, ATT, and/or co-trimoxazole were implicated in 56 of 164 (34%) ADR-related admissions. Seventy-three of 164 (45%) ADRs were assessed as preventable.In our survey, approximately 1 in 12 admissions was because of an ADR. The range of ADRs and implicated drugs reflect South Africa's high HIV and tuberculosis burden. Identification and management of these ADRs should be considered in HIV and tuberculosis care and treatment programs and should be emphasized in health care worker training programmes. |
Multimorbidity patterns in the United States: implications for research and clinical practice
Goodman RA , Ling SM , Briss PA , Parrish RG , Salive ME , Finke BS . J Gerontol A Biol Sci Med Sci 2015 71 (2) 215-20 The increasing prevalence of persons with multimorbidity in many countries has sparked strong growth in research on the epidemiology of multimorbidity, in part to help improve approaches to preventing and managing chronic conditions ( 1–6 ). In this issue of the Journal , Garin and colleagues have made a major contribution to this field of research by examining nationally representative data from studies of noninstitutionalized, predominantly older adults in nine countries that represent the socioeconomic spectrum, and by using a common set of 12 chronic conditions to characterize epidemiologic patterns of multimorbidity among older adults in those countries ( 7 ). | Particularly noteworthy are their results for the relation between multimorbidity and sociodemographic factors (age, sex, education, marital status, wealth, and place of residence), as well as the most prevalent comorbid conditions (hypertension, arthritis, and cataract). In addition, their analysis identified selected multimorbidity combinations for each country and across countries, the most common of which are “cardio-respiratory” and “metabolic” patterns. |
Improving pandemic influenza risk assessment.
Russell CA , Kasson PM , Donis RO , Riley S , Dunbar J , Rambaut A , Asher J , Burke S , Davis CT , Garten RJ , Gnanakaran S , Hay SI , Herfst S , Lewis NS , Lloyd-Smith JO , Macken CA , Maurer-Stroh S , Neuhaus E , Parrish CR , Pepin KM , Shepard SS , Smith DL , Suarez DL , Trock SC , Widdowson MA , George DB , Lipsitch M , Bloom JD . Elife 2014 3 e03883 Assessing the pandemic risk posed by specific non-human influenza A viruses is an important goal in public health research. As influenza virus genome sequencing becomes cheaper, faster, and more readily available, the ability to predict pandemic potential from sequence data could transform pandemic influenza risk assessment capabilities. However, the complexities of the relationships between virus genotype and phenotype make such predictions extremely difficult. The integration of experimental work, computational tool development, and analysis of evolutionary pathways, together with refinements to influenza surveillance, has the potential to transform our ability to assess the risks posed to humans by non-human influenza viruses and lead to improved pandemic preparedness and response. |
Risk factors for delayed initiation of combination antiretroviral therapy in rural north central Nigeria
Aliyu MH , Blevins M , Parrish DD , Megazzini KM , Gebi UI , Muhammad MY , Ahmed ML , Shepherd BE , Hassan A , Vermund SH , Wester CW . J Acquir Immune Defic Syndr 2013 65 (2) e41-9 BACKGROUND: Timely initiation of combination antiretroviral therapy (ART) in eligible HIV-infected patients is associated with substantial reduction in mortality and morbidity. Nigeria has the second largest number of persons living with HIV/AIDS in the world. We examined patient characteristics, time to ART initiation, retention and mortality at five rural facilities in Kwara and Niger states of Nigeria. METHODS: We analyzed program-level cohort data for HIV-infected, ART-naive clients (≥15 years) enrolled from June 2009-February 2011. We modeled the probability of ART initiation among clients meeting national ART eligibility criteria using logistic regression with splines. RESULTS: We enrolled 1,948 ART-naive adults/adolescents into care, of whom 1174 were ART eligible (62% female). Only 74% of eligible patients (n=869) initiated ART within 90 days post-enrollment. The median CD4+ count for eligible clients was 156 cells/microL [IQR: 81-257], with 67% in WHO stage III/IV disease. Adjusting for CD4+ count, WHO stage, functional status, hemoglobin, body mass index, sex, age, education, marital status, employment, clinic of attendance, and month of enrollment, we found that immunosuppression (CD4 350 vs. 200, odds ratio (OR)=2.10 [95%CI: 1.31, 3.35], functional status (bedridden vs. working, OR=4.17 [95%CI: 1.63-10.67]), clinic of attendance (Kuta hospital vs. referent: OR=5.70 [95%CI:2.99-10.89]), and date of enrollment (December 2010 vs. June 2009: OR=2.13 [95%CI:1.19-3.81]) were associated with delayed ART initiation. CONCLUSION: Delayed initiation of ART was associated with higher CD4+ counts, lower functional status, clinic of attendance, and later dates of enrollment among ART-eligible clients. Our findings provide targets for quality improvement efforts that may help reduce attrition and improve ART uptake in similar settings. |
Prevalence of the 23S rRNA A2058G point mutation and molecular subtypes in Treponema pallidum in the United States, 2007 to 2009.
Su JR , Pillay A , Hook EW , Ghanem KG , Wong W , Jackson D , Smith LD , Pierce E , Philip SS , Wilson S , Golden MR , Workowski KA , Chi KH , Parrish DD , Chen CY , Weinstock HS . Sex Transm Dis 2012 39 (10) 794-798 BACKGROUND: The 23S rRNA A2058G point mutation in Treponema pallidum is associated with macrolide antibiotic treatment failure. Its prevalence and potential association with a molecular subtype within the United States are unknown. METHODS: During 2007 to 2009, 11 clinics across the United States sent samples from genital ulcers to the Centers for Disease Control and Prevention. Molecular techniques were used to identify T. pallidum DNA sequences, the A2058G mutation, and subtype of T. pallidum. Accompanying epidemiologic information was abstracted from medical records. RESULTS: A total of 141 samples with T. pallidum were collected from individuals whose median age was 33 years (range, 13-68 years): 118 were male (69% reported as men having sex with men [MSM]). The A2058G mutation was carried in 75 samples (53%) with T. pallidum, with samples from MSM (versus women and other men) more likely carrying the A2058G mutation (65/82 samples versus 8/57 samples; prevalence ratio, 5.7; 95% confidence interval, 2.9-10.8). Of 98 strain-typed samples, 61 (62%) were the 14d9 subtype of T. pallidum, which was also associated with samples with T. pallidum from MSM (prevalence ratio, 3.5; 95% confidence interval, 1.9-6.5). However, among T. pallidum from MSM, the A2058G mutation was not associated with the 14d9 subtype. CONCLUSIONS: The A2058G mutation and 14d9 subtype of T. pallidum were present throughout the United States. Both were more commonly found in T. pallidum from MSM compared with women or other men but were not associated with each other. Treating syphilis with azithromycin should be done cautiously and only when treatment with penicillin or doxycycline is not feasible. (Copyright 2012 American Sexually Transmitted Diseases Association All rights reserved.) |
Probability of negative Mycobacterium tuberculosis complex cultures based on time-to-detection of positive cultures: a multi-center evaluation of commercial broth-based culture systems
Tyrrell FC , Budnick GE , Elliott T , Gillim-Ross L , Hildred MV , Mahlmeister P , Parrish N , Pentella M , Vanneste J , Wang YF , Starks AM . J Clin Microbiol 2012 50 (10) 3275-82 We conducted a multicenter study to determine whether Mycobacterium tuberculosis complex (MTBC) cultures in automated broth-based systems could reliably be considered as negative sooner than six weeks. Laboratory sites used MGIT or BacT/ALERT and tracked results of time to detection of mycobacteria (TTD-all, n = 1547) and MTBC (TTD-MTBC, n = 466) over six-month periods from primarily (93%) respiratory specimens. Cumulative percentages by day detected and median TTD of initial and follow-up specimens were analyzed. The median TTD-MTBC for MGIT (n = 6 sites) was 14 days. For laboratories using standard processing procedures, 100% of MTBC were detected from initial and follow-up specimens in 28 and 35 days, respectively, and no yield of MTBC on solid or MGIT liquid media was observed after five weeks. The median TTD-MTBC for BacT/ALERT (n = 3 sites) was 18 days, with 95% and 100% detected within 37 and 42 days respectively. Analysis of TTD of positive MTBC cultures in broth can predict the probability of culture negativity at defined time points. Receipt of interim negative reports earlier than six weeks could assist clinicians in considering alternative diagnoses, and could alter timing and prioritization of public health interventions. Laboratories should analyze their own TTD data to inform protocol decisions. Laboratories using MGIT could issue no growth of MTBC reports on initial specimens as early as four weeks and on patients undergoing treatment as early as five weeks post-inoculation. |
Inclusion of a CRF01_AE HIV envelope protein boost with a DNA/MVA prime-boost vaccine: impact on humoral and cellular immunogenicity and viral load reduction after SHIV-E challenge
Cox JH , Ferrari MG , Earl P , Lane JR , Jagodzinski LL , Polonis VR , Kuta EG , Boyer JD , Ratto-Kim S , Eller LA , Pham DT , Hart L , Montefiori D , Ferrari G , Parrish S , Weiner DB , Moss B , Kim JH , Birx D , Vancott TC . Vaccine 2012 30 (10) 1830-40 The current study assessed the immunogenicity and protective efficacy of various prime-boost vaccine regimens in rhesus macaques using combinations of recombinant DNA (rDNA), recombinant MVA (rMVA), and subunit gp140 protein. The rDNA and rMVA vectors were constructed to express Env from HIV-1 subtype CRF01_AE and Gag-Pol from CRF01_AE or SIVmac 239. One of the rMVAs, MVA/CMDR, has been recently tested in humans. Immunizations were administered at months 0 and 1 (prime) and months 3 and 6 (boost). After priming, HIV env-specific serum IgG was detected in monkeys receiving gp140 alone or rMVA but not in those receiving rDNA. Titers were enhanced in these groups after boosting either with gp140 alone or with rMVA plus gp140. The groups that received the rDNA prime developed env-specific IgG after boosting with rMVA with or without gp140. HIV Env-specific serum IgG binding antibodies were elicited more frequently and of higher titer, and breadth of neutralizing antibodies was increased with the inclusion of the subunit Env boost. T cell responses were measured by tetramer binding to Gag p11c in Mamu-A*01 macaques, and by IFN-gamma ELISPOT assay to SIV-Gag. T cell responses were induced after vaccination with the highest responses seen in macaques immunized with rDNA and rMVA. Macaques were challenged intravenously with a novel SHIV-E virus (SIVmac239 Gag-Pol with an HIV-1 subtype E-Env CAR402). Post challenge with SHIV-E, antibody titers were boosted in all groups and peaked at 4 weeks. Robust T cell responses were seen in all groups post challenge and in macaques immunized with rDNA and rMVA a clear boosting of responses was seen. A greater than two-log drop in RNA copies/ml at peak viremia and earlier set point was achieved in macaques primed with rDNA, and boosted with rMVA/SHIV-AE plus gp140. Post challenge viremia in macaques immunized with other regimens was not significantly different to that of controls. These results demonstrate that a gp140 subunit and inclusion of SIV Gag-Pol may be critical for control of SHIV post challenge. |
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