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"data_provenance": [ { "name": "genbank" } ], "description": "This phylogeny shows evolutionary relationships of SARS-CoV-2 viruses from the ongoing novel coronavirus COVID-19 pandemic.\n\nAll data we use were deposited in GISAID by scientists around the world.\nWe gratefully acknowledge the authors, originating and submitting laboratories of the genetic sequence and metadata made available through [GISAID](https://gisaid.org) on which this research is based. A full listing of all originating and submitting laboratories is available below. An attribution table is available by clicking on \"Download Data\" at the bottom of the page and then clicking on \"Strain Metadata\" in the resulting dialog box.\n", "display_defaults": { "branch_label": "clade", "color_by": "clade_membership", "distance_measure": "div", "geo_resolution": "region", "map_triplicate": true, "transmission_lines": false }, "filters": [ "region", "country", "division", "new_node", "pango_lineage", "clade_membership" ], "genome_annotations": { "E": { "end": 26472, "seqid": "defaults/reference_seq.gb", "start": 26245, "strand": "+", "type": "CDS" }, "M": { "end": 27191, "seqid": "defaults/reference_seq.gb", "start": 26523, "strand": "+", "type": "CDS" }, "N": { "end": 29533, "seqid": "defaults/reference_seq.gb", "start": 28274, "strand": "+", "type": "CDS" }, "ORF1a": { "end": 13468, "seqid": "defaults/reference_seq.gb", "start": 266, "strand": "+", "type": "CDS" }, "ORF1b": { "end": 21555, "seqid": "defaults/reference_seq.gb", "start": 13468, "strand": "+", 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{ "latitude": 30.451098, "longitude": 86.654576 }, "Europe": { "latitude": 49.646237, "longitude": 10.799454 }, "North America": { "latitude": 28.2367447, "longitude": -97.738017 }, "Oceania": { "latitude": -25.0562891, "longitude": 152.008576 }, "South America": { "latitude": -13.083583, "longitude": -58.470721 } }, "key": "region" } ], "maintainers": [ { "name": "Ivan Aksamentov", "url": "https://neherlab.org" }, { "name": "Richard Neher", "url": "https://neherlab.org" } ], "panels": [ "tree" ], "title": "SARS-CoV-2 phylogeny", "updated": "2021-07-08" }, "tree": { "branch_attrs": { "labels": { "clade": "19A" }, "mutations": {} }, "children": [ { "branch_attrs": { "mutations": {} }, "name": "Wuhan-Hu-1/2019", "node_attrs": { "author": { "author": "Wu et al", "title": "Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome", "value": "Wu et al" }, "clade_membership": { "value": "19A" }, "country": { "confidence": { "China": 1.0 }, "entropy": 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"region": { "value": "North America" }, "region_exposure": { "value": "North America" }, "url": "https://www.ncbi.nlm.nih.gov/nuccore/MW065351" } }, { "branch_attrs": { "mutations": {} }, "name": "CHN/Wuhan_IME-WH02/2019", "node_attrs": { "author": { "author": "Fan et al", "title": "Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/CHN/Wuhan_IME-WH02/2019, complete genome", "value": "Fan et al" }, "clade_membership": { "value": "19A" }, "country": { "confidence": { "China": 1.0 }, "entropy": -1.000088900581841e-12, "value": "China" }, "div": 0, "division": { "value": "Hubei" }, "pango_lineage": { "value": "B" }, "region": { "value": "Asia" }, "region_exposure": { "value": "Asia" }, "url": "https://www.ncbi.nlm.nih.gov/nuccore/MT291827" } }, { "branch_attrs": { "labels": { "aa": "ORF1a: H3233Y; ORF3a: G251V; S: L8V" }, "mutations": { "ORF1a": [ "H3233Y" ], "ORF3a": [ "G251V" ], "S": [ "L8V" ], "nuc": [ "C9962T", "T13929C", "C14724T", "T21584G", "G26144T" ] } }, 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Q1918-, P1919-, Y1920-, P1921-, N1922-, A1923-, S1924-, F1925-, D1926-, N1927-, F1928S, F1930Q, V1931I, D1933*, N1934*, I1935F, F1937P, A1938V, D1939N, D1940W, N1942-, Q1943*, L1944E, G1946C, Y1947F, K1949R, P1950A, A1951*, R1953-, E1954-, L1955-, K1956-, V1957-, T1958Y, F1959I, D1962*, N1964-, G1965-, D1966-, V1967-, V1968-, A1969-, I1970-, D1971-, Y1972-, H1974-, Y1975-, T1976-, P1977-, S1978-, F1979-, K1980-, K1981-, G1982-, A1983-, K1984-, L1985-, L1986-, H1987-, K1988-, P1989*, W1992S, N1995-, N1996-, A1997-, T1998-, N1999-, K2000-, A2001-, T2002-, Y2003-, K2004-, P2005-, N2006-, T2007-, W2008-, C2009*, I2010T, R2011K, C2012Y, W2014V, S2015Y, K2017L, P2018S, V2019L, S2024I, F2025K, D2026F, L2028*, K2029C, S2030T, D2032V, A2033R, Q2034G, G2035R, M2036A, D2037G, A2040*, C2041R, E2042S, D2043S, L2044G, P2046-, V2047-, S2048-, E2049-, E2050-, V2051-, V2052-, E2053-, N2054-, P2055-, T2056-, I2057-, Q2058-, K2059-, D2060-, V2061-, L2062-, E2063-, C2064-, N2065S, V2066Y, K2067H, E2070-, V2071-, V2072-, G2073-, D2074-, I2075-, I2076-, L2077-, K2078-, P2079-, A2080-, N2081-, N2082-, S2083-, L2084-, K2085-, I2086*, E2088-, E2089-, V2090-, G2091-, H2092-, T2093-, D2094-, L2095-, M2096-, A2097-, A2098-, Y2099-, V2100-, D2101-, S2103G, S2104C, T2106S, K2108-, K2109-, P2110-, N2111-, E2112-, L2113-, S2114-, R2115-, V2116-, L2117-, G2118-, L2119-, K2120-, T2121-, L2122-, A2123-, T2124-, H2125-, G2126-, L2127-, A2128R, A2129F, V2130E, V2133-, P2134-, W2135-, D2136-, T2137-, I2138-, A2139-, N2140-, Y2141-, A2142-, K2143-, P2144-, F2145*, K2148Y, V2149*, V2150H, T2152Y, T2154-, N2155-, I2156V, V2157F, T2158K, R2159P, N2162-, R2163-, V2164-, C2165-, T2166-, N2167-, Y2168-, M2169-, P2170-, Y2171-, F2172-, F2173-, T2174Y, L2175*, L2177Y, Q2178A, C2180F, T2181L, F2182Y, T2183F, R2184I, S2185A, S2188*, R2189S, K2191Y, M2194-, P2195-, T2196-, T2197-, I2198-, A2199-, K2200-, N2201-, T2202-, V2203-, K2204-, S2205-, V2206-, G2207-, C2210E, L2211V, E2212T, A2213*, S2214F, N2216*, Y2217T, L2218D, S2220Y, P2221Y, F2223L, S2224V, K2225F, L2226T, N2228K, I2229C, I2230L, I2231P, W2232R, L2234F, L2235N, S2237-, V2238-, C2239-, L2240-, G2241-, S2242-, L2243-, I2244-, Y2245-, S2246-, T2247-, A2248-, A2249-, L2250-, G2251-, V2252-, L2253-, M2254-, S2255L, G2258-, M2259-, P2260-, S2261-, Y2262-, C2263-, T2264-, G2265-, Y2266-, R2267-, E2268-, G2269-, N2272L, S2273Y, T2274W, N2275F, V2276Y, I2278-, A2279-, T2280-, Y2281-, C2282-, T2283-, G2284-, S2285-, I2286-, P2287-, C2288-, S2289L, V2290*, G2294H, D2296-, S2297-, L2298-, D2299-, T2300-, Y2301-, P2302-, S2303-, L2304-, E2305-, T2306-, I2307-, Q2308-, I2309-, T2310-, I2311-, S2313F, K2315F, D2317-, L2318-, T2319-, A2320-, F2321-, G2322-, L2323-, V2324-, A2325-, E2326-, W2327-, F2328-, L2329-, A2330-, Y2331-, I2332-, F2334S, T2335C, F2338H, Y2339*, L2341C, G2342N, L2343H, A2345I, I2346V, M2347F, F2351C, Y2353T, A2355Y, V2356*, H2357*, I2359-, S2360-, N2361-, S2362-, W2363-, L2364-, M2365-, W2366-, L2367-, I2368-, I2369-, N2370-, V2372-, Q2373-, M2374-, A2375-, P2376-, I2377-, S2378-, A2379-, M2380-, V2381-, R2382-, M2383-, Y2384-, I2385-, F2386-, A2388S, S2389Y, F2390G, Y2391*, Y2392N, W2394R, K2395L, S2396*, Y2397F, V2398I, H2399N, V2400L, V2401Y, G2403-, C2404-, N2405-, S2406-, S2407-, T2408-, C2409-, M2410-, M2411-, C2412-, Y2413-, K2414-, R2415-, N2416-, R2417-, A2418-, T2419-, R2420-, E2422L, C2423Q, T2425*, I2426*, V2427S, G2429K, V2430S, R2432M, S2433Y, F2434N, V2436L, Y2437L, A2438Q, N2439T, G2440T, G2441Q, K2442L, G2443E, F2444L, K2446*, H2448-, N2449-, W2450-, N2451-, C2452-, V2453-, N2454-, C2455-, D2456-, T2457-, F2458-, C2459-, A2460-, G2461-, S2462-, T2463*, F2464Y, D2467C, A2470-, R2471-, D2472-, L2473-, S2474-, L2475-, Q2476-, F2477-, K2478-, R2479-, P2480-, I2481-, N2482*, P2483K, D2485N, Q2486K, S2488Y, Y2489*, I2490P, D2492P, V2494L, T2495L, V2496*, K2497*, N2498S, G2499W, I2501-, H2502-, L2503-, Y2504-, F2505-, D2506-, A2508D, G2509L, Q2510*, Y2513-, E2514-, R2515-, H2516F, H2520-, F2521-, V2522-, N2523-, L2524F, D2525C, N2526*, N2530-, N2531-, T2532-, K2533-, G2534-, S2535-, L2536-, P2537-, I2538-, N2539-, V2540-, I2541-, V2542-, F2543-, D2544-, G2545-, K2546-, K2548V, E2550L, E2551L, S2552Q, K2555-, S2556-, A2557-, S2558-, V2559-, Y2561V, Q2563-, L2564-, M2565-, C2566-, Q2567-, P2568-, I2569-, L2570-, L2571-, L2572-, D2573-, Q2574T, A2575Y, L2576T, S2578T, D2579R, V2580S, D2582I, A2584-, E2585-, V2586-, A2587-, K2589Y, M2590V, D2592I, A2593N, Y2594F, V2595*, N2596R, F2598N, S2599G, S2600K, F2602Q, V2604-, P2605-, M2606-, E2607-, K2608-, L2609-, K2610-, T2611-, L2612-, V2613-, A2614-, A2616K, A2618-, E2619-, L2620-, A2621-, K2622-, N2623-, V2624-, S2625-, L2626-, D2627-, N2628C, S2631F, T2632Y, I2634S, A2636S, Q2639-, G2640-, F2641-, V2642-, D2643-, S2644-, D2645-, V2646-, E2647-, T2648-, K2649-, D2650-, V2652-, E2653-, C2654-, L2655-, K2656-, L2657-, S2658-, H2659-, Q2660-, S2661-, D2662-, I2663-, E2664-, G2667S, D2668I, S2669*, C2670H, N2671R, N2672S, M2674-, L2675-, T2676-, Y2677-, N2678-, K2679-, V2680-, E2681-, N2682-, M2683D, R2686*, D2687P, L2688W, G2689C, A2690L, C2691Y, I2692*, D2693L, C2694*, S2695C, R2697S, H2698Y, I2699*, N2700C, Q2702G, V2703S, A2704K, H2707-, N2708-, I2709-, A2710-, L2711-, I2712-, W2713-, N2714-, V2715-, K2716-, D2717Q, F2718H, M2719C, S2720F, L2721D, S2722M, Q2724R, L2725*, Q2728-, I2729-, R2730-, S2731-, A2732-, A2733-, K2734-, K2735-, N2736-, N2737-, L2738-, P2739-, F2740E, K2741*, A2745-, T2746-, T2747-, R2748-, Q2749-, V2750-, V2751-, N2752-, V2753-, V2754-, T2755-, T2756-, K2757-, I2758-, A2759-, L2760-, K2761-, G2762N, G2763N, I2765A, N2768-, W2769-, L2770-, K2771-, Q2772-, L2773-, I2774*, K2775S, V2776Y, L2778C, V2783-, A2784-, A2785-, I2786-, F2787-, Y2788-, L2789-, I2790-, T2791-, P2792-, V2793-, H2794-, V2795-, M2796-, S2797-, K2798-, H2799-, T2800N, D2801N, F2802T, S2803C, E2805R, I2807Q, K2810-, A2811-, I2812-, D2813-, G2814-, G2815-, V2816-, T2817-, R2818-, D2819-, I2820-, A2821-, S2822-, T2823*, D2824Q, F2827*, A2828F, N2829*, K2830H, H2831M, A2832V, D2833*, F2834P, D2835A, T2836W, F2838*, S2839L, Q2840Y, R2841*, G2842*, G2843Q, Y2845L, T2846P, N2847I, K2849-, A2850-, C2851-, P2852-, L2853-, I2854-, A2855-, A2856-, V2857-, I2858-, T2859-, R2860-, E2861-, V2862-, V2865-, V2866-, P2867-, G2868-, L2869-, P2870-, G2871-, T2872-, I2873-, L2874C, T2877H, G2879*, D2880W, F2881*, H2883A, P2886T, R2887*, V2888S, S2890-, A2891-, V2892-, G2893-, N2894-, I2895*, T2898R, P2899V, S2900H, K2901*, I2903-, E2904-, Y2905-, T2906-, D2907-, F2908-, A2909-, T2910-, S2911-, A2912-, C2913-, V2914-, L2915-, A2916-, A2917-, E2918-, T2920N, K2923W, D2924*, G2927-, K2928-, P2929-, V2930-, P2931-, Y2932-, C2933-, Y2934-, D2935-, N2937I, V2938L, E2940-, G2941-, S2942-, V2943-, A2944*, E2946Q, S2947C, L2948T, P2950-, D2951-, T2952-, R2953-, Y2954-, V2955-, L2956-, M2957-, D2958-, G2959-, S2960-, I2961-, I2962-, Q2963-, F2964-, P2965-, N2966-, T2967-, Y2968-, E2970Y, G2971Y, R2974-, V2975-, V2976-, T2977-, T2978-, F2979-, D2980-, S2981-, E2982L, Y2983*, C2984A, G2987L, T2988*, C2989K, E2990I, E2993-, A2994-, G2995-, V2996-, C2997-, V2998-, S2999-, T3000-, S3001-, G3002-, R3003-, V3005*, N3007L, N3008Q, D3009I, Y3010F, Y3011T, L3014-, P3015-, G3016-, V3017-, F3018-, C3019-, G3020-, V3021-, D3022-, A3023-, V3024-, N3025-, L3026F, M3030-, F3031-, T3032-, P3033-, L3034-, I3035-, Q3036-, P3037-, I3038-, G3039-, A3040-, L3041-, D3042-, I3043-, A3045T, S3046Y, I3047W, V3048C, A3049F, G3051H, V3053Y, A3054R, I3055S, V3056N, V3057M, T3058P, A3061-, Y3062-, Y3063-, F3064-, M3065-, R3066-, F3067-, R3068-, R3069-, A3070L, G3072Y, S3075-, H3076-, V3077-, V3078-, A3079-, F3080-, N3081-, T3082-, L3083-, L3084-, F3085-, L3086-, M3087-, S3088-, V3091L, C3093I, P3096-, V3097-, Y3098-, S3099-, F3100-, L3101-, P3102-, G3103-, V3104-, Y3105-, S3106-, V3107-, I3108-, Y3109-, L3110W, Y3111C, T3113F, F3114C, N3118Y, D3119S, S3121D, F3122G, L3123Y, A3124V, I3126-, Q3127-, W3128-, M3129-, V3130-, M3131-, F3132-, T3133-, P3134-, L3135-, V3136-, P3137-, F3138-, W3139-, I3140-, I3142K, Y3144-, I3145-, I3146-, C3147-, I3148-, S3149-, T3150-, K3151-, H3152-, F3153-, Y3154-, W3155-, F3156-, F3157-, S3158-, N3159-, Y3160-, L3161-, K3162-, R3163F, R3164L, V3165L, F3167L, N3168*, G3169*, V3170L, S3171P, F3172K, S3173E, E3176-, E3177-, A3178-, A3179-, L3180-, C3181-, T3182-, F3183-, L3184-, L3185-, N3186-, K3187-, E3188-, M3189-, Y3190-, L3191V, L3193*, D3196-, V3197-, L3198-, L3199-, P3200-, L3201-, T3202-, Q3203-, Y3204-, N3205-, R3206-, Y3207-, L3208-, A3209-, L3210-, K3213G, K3215-, Y3216-, F3217-, S3218-, G3219-, A3220-, M3221-, D3222-, T3223-, T3224-, S3225-, Y3226-, R3227-, E3228-, A3229-, A3230-, C3231-, C3232N, H3233*, A3235Q, K3236R, A3237S, L3238C, N3239L, D3240L, F3241S, N3243R, S3244K, D3247T, V3248N, Q3251-, P3252-, P3253-, Q3254-, T3255-, S3256-, I3257-, T3258-, S3259-, A3260-, V3261-, L3262H, Q3263L, G3265W, R3267*, M3269N, A3270G, F3271I, G3274-, K3275-, V3276-, E3277-, G3278-, C3279-, M3280-, V3281-, Q3282-, V3283-, T3284-, C3285-, G3286-, T3287-, T3288-, T3289-, L3290-, N3291-, G3292N, D3296-, D3297-, V3298-, V3299-, Y3300-, C3301-, P3302-, R3303-, H3304-, V3305-, I3306S, C3307K, S3309C, E3310D, D3311L, M3312H, N3314*, P3315R, N3316H, Y3317A, E3318*, D3319P, L3320*, I3322*, K3324-, S3325-, N3326-, H3327-, N3328-, F3329-, L3330-, V3331-, Q3332-, A3333-, G3334-, N3335-, V3336-, Q3337-, L3338-, R3339-, V3340-, I3341W, G3342*, H3343C, M3345T, N3347T, C3348F, V3349Y, L3350A, K3353*, D3355*, T3356V, A3357C, N3358S, P3359H, K3360S, P3362R, K3363T, Y3364D, K3365F, V3367-, R3368-, I3369-, Q3370-, P3371-, G3372-, Q3373-, T3374-, F3375-, S3376-, V3377-, L3378-, A3379-, C3380-, Y3381-, N3382-, G3383-, P3385V, G3387F, V3388H, Q3390-, C3391-, A3392-, M3393-, R3394-, P3395-, N3396-, F3397-, T3398-, I3399-, K3400-, G3401-, S3402-, F3403-, L3404-, N3405-, G3406-, S3407-, C3408*, S3410L, V3411C, G3412L, N3414-, I3415-, D3416-, Y3417-, D3418-, C3419-, V3420-, S3421-, F3422-, C3423-, Y3424-, M3425-, H3426-, H3427-, M3428-, E3429-, L3430-, P3431-, T3432-, G3433L, V3434L, G3437W, D3439-, L3440-, E3441-, G3442-, N3443-, F3444-, Y3445-, G3446-, P3447-, F3448-, V3449-, D3450-, R3451-, Q3452F, T3453C, A3454*, A3457N, G3458S, D3460S, T3461S, T3462W, I3463Y, T3464G, V3465H, V3467Y, L3468Y, A3469S, W3470*, L3471C, Y3472F, A3473S, A3474L, N3477-, G3478-, D3479-, R3480-, W3481-, F3482-, L3483-, N3484-, R3485-, F3486-, T3487-, T3488-, T3489Y, L3490H, D3492S, F3493*, N3494*, V3496*, A3497P, M3498C, K3499G, Y3502T, E3503R, L3505-, T3506-, Q3507-, D3508-, H3509-, V3510-, D3511-, I3512-, L3513-, G3514-, P3515-, L3516-, S3517C, A3518*, Q3519H, G3521F, A3523-, V3524-, L3525-, D3526-, M3527-, C3528-, A3529-, S3530-, L3531-, K3532-, E3533-, L3534-, L3535-, Q3536-, N3537-, G3538-, M3539-, N3540-, G3541K, T3543F, L3545-, G3546-, S3547-, A3548-, L3549-, L3550-, E3551-, D3552-, E3553-, F3554-, T3555-, P3556-, F3557-, D3558-, V3559-, V3560-, Q3562K, G3565E, V3566K, T3567N, F3568N, S3570-, A3571-, V3572-, K3573-, R3574-, T3575-, I3576-, K3577-, G3578-, T3579-, H3580-, H3581-, W3582-, L3583-, L3584-, L3585-, T3586-, I3587G, L3588Y, S3590P, L3592F, V3595-, Q3596-, S3597-, T3598-, Q3599-, W3600-, S3601-, L3602-, F3603-, F3604-, Q3777H, T4249I; ORF7b: C41F" }, "mutations": { "ORF1a": [ "G519-", "A520-", "W521-", "N522-", "I523-", "G524-", "E525-", "Q526V", "K527P", "S528G", "S531R", "P532L", "Y534-", "A535-", "F536-", "A537-", "S538-", "E539-", "A540-", "A541-", "R542-", "V543-", "V544-", "R545-", "S546-", "I547-", "F548-", "S549-", "R550-", "T551-", "L552V", "E553L", "T554Y", "A555D", "N557F", "V559R", "V561P", "Q563-", "K564-", "A565-", "A566-", "I567-", "T568-", "I569-", "L570-", "D571-", "G572-", "I573-", "S574*", "R579H", "D582-", "A583-", "M584-", "M585-", "F586-", "T587-", "S588-", "D589W", "A591L", "N593I", "N594*", "V596-", "V597-", "M598-", "A599*", "Y600W", "I601P", "G603L", "G604Q", "Q607*", "Q611-", "W612-", "L613-", "T614-", "N615-", "I616-", "F617-", "G618-", "T619-", "V620-", "Y621-", "E622-", "K623-", "K625N", "V627S", "D629I", "W630G", "E632V", "E633*", "K634S", "K636L", "G638T", "E640G", "F641K", "R643L", "D644N", "G645L", "W646S", "E647Q", "I648P", "K650-", "F651-", "I652-", "S653-", "T654-", "C655-", "A656-", "C657-", "E658-", "I659-", "V660-", "G661-", "G662-", "Q663-", "I664L", "T666K", "C667L", "A668S", "K669V", "E670D", "I671K", "K672L", "E673S", "S674P", "T677I", "F678N", "K680W", "V682C", "N683V", "K684L", "F685T", "A687S", "C689-", "A690-", "D691-", "S692-", "I693-", "I694-", "I695-", "G696-", "G697-", "A698-", "K699-", "K701V", "A702E", "G706P", "E707*", "T708I", "F709*", "T711K", "S713L", "K714S", "G715R", "L716T", "Y717Q", "K719D", "V721T", "K722E", "R724-", "E725-", "E726-", "T727-", "G728-", "L729V", "M731N", "K734S", "A735S", "P736*", "K737R", "I739K", "I740H", "L742-", "E743-", "G744-", "E745-", "T746-", "L747-", "P748-", "T749-", "E750-", "V751-", "L752-", "T753-", "E754-", "E755-", "V756-", "V757P", "L758Q", "T760N", "G761N", 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