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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: shapiro bj. Microb Genom. 2024 Oct;10(10):001293. doi: 10.1099/mgen.0.001293. Microb Genom. 2024. PMID: 39401061 Free PMC article.
Combining Short- and Long-Read Sequencing Technologies to Identify SARS-CoV-2 Variants in Wastewater.
Jayme G, Liu JL, Galvez JH, Reiling SJ, Celikkol S, N'Guessan A, Lee S, Chen SH, Tsitouras A, Sanchez-Quete F, Maere T, Goitom E, Hachad M, Mercier E, Loeb SK, Vanrolleghem PA, Dorner S, Delatolla R, Shapiro BJ, Frigon D, Ragoussis J, Snutch TP. Jayme G, et al. Among authors: shapiro bj. Viruses. 2024 Sep 21;16(9):1495. doi: 10.3390/v16091495. Viruses. 2024. PMID: 39339971 Free PMC article.
Vibrio cholerae O1 experiences mild bottlenecks through the gastrointestinal tract in some but not all cholera patients.
Lypaczewski P, Chac D, Dunmire CN, Tandoc KM, Chowdhury F, Khan AI, Bhuiyan TR, Harris JB, LaRocque RC, Calderwood SB, Ryan ET, Qadri F, Shapiro BJ, Weil AA. Lypaczewski P, et al. Among authors: shapiro bj. Microbiol Spectr. 2024 Aug 6;12(8):e0078524. doi: 10.1128/spectrum.00785-24. Epub 2024 Jun 25. Microbiol Spectr. 2024. PMID: 38916318 Free PMC article.
Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data.
Sutcliffe SG, Kraemer SA, Ellmen I, Knapp JJ, Overton AK, Nash D, Nissimov JI, Charles TC, Dreifuss D, Topolsky I, Baykal PI, Fuhrmann L, Jablonski KP, Beerenwinkel N, Levy JI, Olabode AS, Becker DG, Gugan G, Brintnell E, Poon AFY, Valieris R, Drummond RD, Defelicibus A, Dias-Neto E, Rosales RA, Tojal da Silva I, Orfanou A, Psomopoulos F, Pechlivanis N, Pipes L, Chen Z, Baaijens JA, Baym M, Shapiro BJ. Sutcliffe SG, et al. Among authors: shapiro bj. Microb Genom. 2024 May;10(5):001249. doi: 10.1099/mgen.0.001249. Microb Genom. 2024. PMID: 38785221 Free PMC article.
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: shapiro bj. 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.
Phage predation, disease severity, and pathogen genetic diversity in cholera patients.
Madi N, Cato ET, Abu Sayeed M, Creasy-Marrazzo A, Cuénod A, Islam K, Khabir MIU, Bhuiyan MTR, Begum YA, Freeman E, Vustepalli A, Brinkley L, Kamat M, Bailey LS, Basso KB, Qadri F, Khan AI, Shapiro BJ, Nelson EJ. Madi N, et al. Among authors: shapiro bj. Science. 2024 Apr 19;384(6693):eadj3166. doi: 10.1126/science.adj3166. Epub 2024 Apr 19. Science. 2024. PMID: 38669570
Snapshot of cyanobacterial toxins in Pakistani freshwater bodies.
Batool U, Tromas N, Simon DF, Sauvé S, Shapiro BJ, Ahmed M. Batool U, et al. Among authors: shapiro bj. Environ Sci Pollut Res Int. 2024 Apr;31(16):24648-24661. doi: 10.1007/s11356-024-32744-w. Epub 2024 Mar 6. Environ Sci Pollut Res Int. 2024. PMID: 38448773
Diversity of Vibrio cholerae O1 through the human gastrointestinal tract during cholera.
Lypaczewski P, Chac D, Dunmire CN, Tandoc KM, Chowdhury F, Khan AI, Bhuiyan T, Harris JB, LaRocque RC, Calderwood SB, Ryan ET, Qadri F, Shapiro BJ, Weil AA. Lypaczewski P, et al. Among authors: shapiro bj. bioRxiv [Preprint]. 2024 Feb 8:2024.02.08.579476. doi: 10.1101/2024.02.08.579476. bioRxiv. 2024. Update in: Microbiol Spectr. 2024 Aug 6;12(8):e0078524. doi: 10.1128/spectrum.00785-24 PMID: 38370713 Free PMC article. Updated. Preprint.
125 results