Author: Daniel J Butler; Christopher Mozsary; Cem Meydan; David C Danko; Jonathan Foox; Joel Rosiene; Alon Shaiber; Ebrahim Afshinnekoo; Matthew MacKay; Fritz J Sedlazeck; Nikolay A Ivanov; Maria A Sierra; Diana Pohle; Michael Zeitz; Vijendra Ramlall; Undina Gisladottir; Craig D Westover; Krista Ryon; Benjamin Young; Chandrima Bhattacharya; Phyllis Ruggiero; Bradley W Langhorst; Nathan A Tanner; Justyn Gawrys; Dmitry Meleshko; Dong Xu; Jenny Xiang; Angelika Iftner; Daniela Bezdan; John Sipley; Lin Cong; Arryn Craney; Priya Velu; Ari Melnick; Iman A Hajirasouliha; Thomas Iftner; Mirella Salvatore; Massimo Loda; Lars F Westblade; Shawn Levy; Melissa Cushing; Nicholas P Tatonetti; Marcin Imielinski; Hanna Rennert; Christopher Mason
Title: Host, Viral, and Environmental Transcriptome Profiles of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Document date: 2020_4_20
ID: kyoa5gsf_19
Snippet: Analyzing groupings obtained from the Nextstrain-derived maximum likelihood phylogenetic tree, we found a high proportion (>83%) of our samples were associated with A2a, a large Western European derived clade that comprises nearly half of the sequences in GISAID. These results validate recently published findings (Gonzalez-Reiche et al., 2020) . In addition, we found additional samples from clades with mixed Asian and European sources (A1a, 7% of.....
Document: Analyzing groupings obtained from the Nextstrain-derived maximum likelihood phylogenetic tree, we found a high proportion (>83%) of our samples were associated with A2a, a large Western European derived clade that comprises nearly half of the sequences in GISAID. These results validate recently published findings (Gonzalez-Reiche et al., 2020) . In addition, we found additional samples from clades with mixed Asian and European sources (A1a, 7% of cases; B1, 3% of cases; B, 1% of cases; 4% of cases unassigned). Among these, we identified a clear predominance (90%) of the "L" strain, which is defined by a reference base at position 28143 (ORF8) and previously associated with severe cases in Wuhan (Tang et al., 2020) (Figure 4b) .
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