Viruses with tyrosine (Y) at Spike 655 are colored in yellow. quality sequences are demonstrated by the gaps in data (i.e. cat 3 day time 6 and cat 4 day time 9).(TIF) ppat.1009373.s002.tif (1018K) GUID:?ACD9FF2F-7509-4842-A552-1FF4596B1592 S3 Fig: Longitudinal frequency of indels detected in all pet cats and at all timepoints. Each indel is definitely coloured based on gene location. Days with viral lots too low to yield high quality sequences are demonstrated by the gaps in data (i.e. cat 3 day time 6 and cat 4 day time 9). Notice the y-axis range is definitely 0C12%, not 0C100%, to facilitate readability.(TIF) ppat.1009373.s003.tif (60M) GUID:?23159401-40E8-4CFF-9808-146E71E2264E S4 Fig: Sequence alignment of all tiger, lion, and home cat sequences available in GISAID as of December 2020. Sequences were aligned against “type”:”entrez-nucleotide”,”attrs”:”text”:”MW219695.1″,”term_id”:”1928805944″,”term_text”:”MW219695.1″MW219695.1, the inoculum computer virus used in these experiments. Consensus-level variations are highlighted having a blue vertical marker. Indels are mentioned having a horizontal vertical marker. The spike open reading frame is definitely annotated having a green marker and site amino acid 655 in Spike is definitely highlighted with the orange package. None of them of these sequences contain a consensus mutation at residue 655 in Spike.(TIF) ppat.1009373.s004.tif (514K) GUID:?5F436AE1-27FA-43B9-AC3D-B31EDEF6AB8A S5 Fig: Geographic dispersion of Spike H655Y variant. A) A time-resolved phylogeny focused on viruses that contain Spike H655Y. Viruses that contain histidine (H) at Spike 655 are coloured in teal. Viruses with tyrosine (Y) at Spike 655 are coloured in yellow. B) Counts of SARS-CoV-2 viruses that contain Spike H655Y, broken down by country. C) Map highlighting the number viruses from each country. The size of the circle represents the number of sequences from the appropriate country contained in the phylogeny.(TIF) ppat.1009373.s005.tif (1.8M) GUID:?D4E7728E-95B0-4CF4-B706-1F0B45776A66 S6 Fig: Go through depth across the SARS-CoV-2 genome in index pet cats. Each day is definitely displayed by a Primaquine Diphosphate different color. Replicate A is definitely demonstrated in the remaining column and replicate B is definitely demonstrated in the right column.(TIF) ppat.1009373.s006.tif (1.9M) GUID:?7CD5934B-733D-48E6-BE6A-4BAC303471CC S7 Fig: Read depth across the SARS-CoV-2 genome in contact cats. Each day is definitely represented by a different color. Replicate A is Primaquine Diphosphate Rabbit Polyclonal to Mammaglobin B definitely demonstrated in the remaining column and replicate B is definitely demonstrated in the right column.(TIF) ppat.1009373.s007.tif (3.6M) GUID:?9F710D96-CE53-4E9F-A3AD-1D06E1928D70 S8 Fig: Intersection variants found across complex replicates in index pet cats. The frequency of each variant per replicate is definitely demonstrated here. The diagonal collection represents the 1:1 intersection of replicate variants. The subplot to the right of each primary plot is definitely a zoomed-in look Primaquine Diphosphate at of the low-frequency variants (3C15%). Each timepoint is definitely denoted by a different color.(TIF) ppat.1009373.s008.tif (1.0M) GUID:?23CC9F99-CFE4-4BFF-9B7B-79714DC3CA11 S9 Fig: Intersection variants found across technical replicates in contact pet cats. The frequency of each variant per replicate is definitely demonstrated here. The diagonal collection represents the 1:1 intersection of replicate variants. The subplot to the right of each primary plot is definitely a zoomed-in look at of the low-frequency variants (3C15%). Each timepoint is definitely denoted by a different color.(TIF) ppat.1009373.s009.tif (988K) GUID:?456B3B3E-EEDB-4D25-B0BA-7FE4200D4AA9 S10 Fig: Longitudinal pairwise nonsynonymous nucleotide diversity divided by pairwise synonymous nucleotide diversity in index cats. Collection color denotes gene. The horizontal dotted gray line is definitely plotted at = 1 or when N ~ S.(TIF) ppat.1009373.s010.tif (547K) GUID:?EE35FFC5-3305-49BE-A3DD-77581B701FDB S11 Fig: Longitudinal pairwise nonsynonymous nucleotide diversity divided by pairwise synonymous nucleotide diversity in contact pet cats. Collection color denotes gene. The horizontal dotted gray line is definitely plotted at Primaquine Diphosphate = 1 or when N ~ S.(TIF) ppat.1009373.s011.tif (533K) GUID:?014F453E-1B1F-4A73-8666-CC5938F21D1D S12 Fig: SARS-CoV-2 spike glycoprotein crystal structure. Spike H655Y is definitely highlighted in blue. The table to the right of the crystal structure includes summary info regarding the effect of a histidine to tyrosine switch on amino acid charge, volume, and aromaticity. * Qualitative meanings of radical amino acid replacements, based on three alternate residue groupings, observe Hanada et al., 2006 [68]. The crystal structure and summary info were generated using GISAIDs CoVserver mutation analysis tool.(TIF) ppat.1009373.s012.tif (22M) GUID:?55DD971E-8AF9-41B3-90C6-2342CD0CCC99 S1 Table: Nonsynonymous and synonymous nucleotide diversity estimates in index cats. (PDF) ppat.1009373.s013.pdf (70K) GUID:?BC259045-CB8C-43CD-9DA8-F9302B9E47C0 S2 Table: Genome-wide pairwise nucleotide diversity estimations in index and contact pet cats. (PDF) ppat.1009373.s014.pdf (37K) GUID:?1E31236E-EBB9-48C3-BE31-4F54711EA2EF S3 Table: ARTIC v3 primer sequences. (PDF) ppat.1009373.s015.pdf (117K) GUID:?14F16BCB-3E02-4143-AA4B-523D3D14D210 Attachment: Submitted filename: = 1 or when N ~ S. (TIF) Click here for more data file.(547K, tif) S11 FigLongitudinal pairwise nonsynonymous nucleotide diversity divided by pairwise synonymous nucleotide diversity in contact pet cats. Collection color denotes gene. The horizontal dotted gray line is definitely plotted at = 1 or when N ~ S. (TIF) Click here for more data file.(533K, tif) S12 FigSARS-CoV-2 spike glycoprotein crystal structure. Spike H655Y is definitely highlighted in blue. The table to the right of the crystal structure includes summary info regarding Primaquine Diphosphate the effect of a histidine to tyrosine switch on amino.