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The Canadian VirusSeq Data Portal & Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology.
Gill EE, Jia B, Murall CL, Poujol R, Anwar MZ, John NS, Richardsson J, Hobb A, Olabode AS, Lepsa A, Duggan AT, Tyler AD, N'Guessan A, Kachru A, Chan B, Yoshida C, Yung CK, Bujold D, Andric D, Su E, Griffiths EJ, Van Domselaar G, Jolly GW, Ward HKE, Feher H, Baker J, Simpson JT, Uddin J, Ragoussis J, Eubank J, Fritz JH, Gálvez JH, Fang K, Cullion K, Rivera L, Xiang L, Croxen MA, Shiell M, Prystajecky N, Quirion PO, Bajari R, Rich S, Mubareka S, Moreira S, Cain S, Sutcliffe SG, Kraemer SA, Joly Y, Alturmessov Y, Consortium C, Consortium C; VirusSeq Data Portal Academic and Health network; Fiume M, Snutch TP, Bell C, Lopez-Correa C, Hussin JG, Joy JB, Colijn C, Gordon PMK, Hsiao WWL, Poon AFY, Knox NC, Courtot M, Stein L, Otto SP, Bourque G, Shapiro BJ, Brinkman FSL. Gill EE, et al. Among authors: joy jb. ArXiv [Preprint]. 2024 May 8:arXiv:2405.04734v1. ArXiv. 2024. Update in: Microb Genom. 2024 Oct;10(10). doi: 10.1099/mgen.0.001293 PMID: 38764594 Free PMC article. Updated. Preprint.
Longitudinal screening of retail milk from Canadian provinces reveals no detections of influenza A virus RNA (April-July 2024): leveraging a newly established pan-Canadian network for responding to emerging viruses.
Wallace HL, Wight J, Baz M, Dowding B, Flamand L, Hobman T, Jean F, Joy JB, Lang AS, MacParland S, McCormick C, Noyce R, Russell RS, Sagan SM, Snyman J, Rzeszutek GJ, Jafri MS, Bogoch I, Kindrachuk J, Rasmussen AL. Wallace HL, et al. Among authors: joy jb. Can J Microbiol. 2024 Sep 27. doi: 10.1139/cjm-2024-0120. Online ahead of print. Can J Microbiol. 2024. PMID: 39332021 Free article.
The Canadian VirusSeq Data Portal and Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology.
Gill EE, Jia B, Murall CL, Poujol R, Anwar MZ, John NS, Richardsson J, Hobb A, Olabode AS, Lepsa A, Duggan AT, Tyler AD, N'Guessan A, Kachru A, Chan B, Yoshida C, Yung CK, Bujold D, Andric D, Su E, Griffiths EJ, Van Domselaar G, Jolly GW, Ward HKE, Feher H, Baker J, Simpson JT, Uddin J, Ragoussis J, Eubank J, Fritz JH, Gálvez JH, Fang K, Cullion K, Rivera L, Xiang L, Croxen MA, Shiell M, Prystajecky N, Quirion PO, Bajari R, Rich S, Mubareka S, Moreira S, Cain S, Sutcliffe SG, Kraemer SA, Alturmessov Y, Joly Y, Cphln Consortium, CanCOGeN Consortium, VirusSeq Data Portal Academic And Health Network, Fiume M, Snutch TP, Bell C, Lopez-Correa C, Hussin JG, Joy JB, Colijn C, Gordon PMK, Hsiao WWL, Poon AFY, Knox NC, Courtot M, Stein L, Otto SP, Bourque G, Shapiro BJ, Brinkman FSL. Gill EE, et al. Among authors: joy jb. Microb Genom. 2024 Oct;10(10):001293. doi: 10.1099/mgen.0.001293. Microb Genom. 2024. PMID: 39401061 Free PMC article.
A simple phylogenetic approach to analyze hypermutated HIV proviruses reveals insights into their dynamics and persistence during antiretroviral therapy.
Shahid A, Jones BR, Duncan MC, MacLennan S, Dapp MJ, Kuniholm MH, Aouizerat B, Archin NM, Gange S, Ofotokun I, Fischl MA, Kassaye S, Goldstein H, Anastos K, Joy JB, Brumme ZL. Shahid A, et al. Among authors: joy jb. Res Sq [Preprint]. 2024 Jun 13:rs.3.rs-4549934. doi: 10.21203/rs.3.rs-4549934/v1. Res Sq. 2024. PMID: 38947061 Free PMC article. Preprint.
Longitudinal evolution of the HIV effective reproduction number following sequential expansion of treatment as prevention and pre-exposure prophylaxis in British Columbia, Canada: a population-level programme evaluation.
Lima VD, Zhu J, Barrios R, Toy J, Joy JB, Williams BG, Granich R, Wu Z, Wong J, Montaner JSG. Lima VD, et al. Among authors: joy jb. Lancet HIV. 2024 Jul;11(7):e461-e469. doi: 10.1016/S2352-3018(24)00094-8. Epub 2024 Jun 4. Lancet HIV. 2024. PMID: 38848736
The replication-competent HIV reservoir is a genetically restricted, younger subset of the overall pool of HIV proviruses persisting during therapy, which is highly genetically stable over time.
Shahid A, MacLennan S, Jones BR, Sudderuddin H, Dang Z, Cobarrubias K, Duncan MC, Kinloch NN, Dapp MJ, Archin NM, Fischl MA, Ofotokun I, Adimora A, Gange S, Aouizerat B, Kuniholm MH, Kassaye S, Mullins JI, Goldstein H, Joy JB, Anastos K, Brumme ZL; MACS/WIHS combined cohort study (MWCSS). Shahid A, et al. Among authors: joy jb. J Virol. 2024 Feb 20;98(2):e0165523. doi: 10.1128/jvi.01655-23. Epub 2024 Jan 12. J Virol. 2024. PMID: 38214547 Free PMC article.
HIV reservoirs are dominated by genetically younger and clonally enriched proviruses.
Kinloch NN, Shahid A, Dong W, Kirkby D, Jones BR, Beelen CJ, MacMillan D, Lee GQ, Mota TM, Sudderuddin H, Barad E, Harris M, Brumme CJ, Jones RB, Brockman MA, Joy JB, Brumme ZL. Kinloch NN, et al. Among authors: joy jb. mBio. 2023 Dec 19;14(6):e0241723. doi: 10.1128/mbio.02417-23. Epub 2023 Nov 16. mBio. 2023. PMID: 37971267 Free PMC article.
Community Insights in Phylogenetic HIV Research: The CIPHR Project Protocol.
Cholette F, Lazarus L, Macharia P, Thompson LH, Githaiga S, Mathenge J, Walimbwa J, Kuria I, Okoth S, Wambua S, Albert H, Mwangi P, Adhiambo J, Kasiba R, Juma E, Battacharjee P, Kimani J, Sandstrom P, Meyers AFA, Joy JB, Thomann M, McLaren PJ, Shaw S, Mishra S, Becker ML, McKinnon L, Lorway R. Cholette F, et al. Among authors: joy jb. Glob Public Health. 2023 Jan;18(1):2269435. doi: 10.1080/17441692.2023.2269435. Epub 2023 Oct 18. Glob Public Health. 2023. PMID: 37851872 Free article.
The replication-competent HIV reservoir is a genetically restricted, younger subset of the overall pool of HIV proviruses persisting during therapy, which is highly genetically stable over time.
Shahid A, MacLennan S, Jones BR, Sudderuddin H, Dang Z, Cobamibias K, Duncan MC, Kinloch NN, Dapp MJ, Archin NM, Fischl MA, Ofotokun I, Adimora A, Gange S, Aouizerat B, Kuniholm MH, Kassaye S, Mullins JI, Goldstein H, Joy JB, Anastos K, Brumme ZL. Shahid A, et al. Among authors: joy jb. Res Sq [Preprint]. 2023 Aug 16:rs.3.rs-3259040. doi: 10.21203/rs.3.rs-3259040/v1. Res Sq. 2023. Update in: J Virol. 2024 Feb 20;98(2):e0165523. doi: 10.1128/jvi.01655-23 PMID: 37645749 Free PMC article. Updated. Preprint.
63 results