Supplemental Figures - JCI Insight

Supplemental Figures

Supplemental Figure 1. Positive diagnoses by first three digits of zip code. Outlined regions correspond to areas sharing the first three digits of their zip code (Washington, DC outlined in black, all others grey). Each region is shaded by the number of patients with positive COVID-19 diagnoses in March 2020 (from the Johns Hopkins Health System) reporting home residence in that region. Regions with 1–5 positive diagnoses are shown as 5.

Supplemental Figure 2. Single nucleotide polymorphisms present in three or more JHHS sequences. Rows = samples sequenced as part of this study (114), sorted by Pangolin lineage. Columns = positions with consensus variants in three or more sequences. Black cells = variant present; grey cells = ambiguity present. Columns are clustered using complete linkage hierarchical clustering. JHHS lineages are sub-groups of pangolin lineages in which two or more variants are shared between three or more JHHS sequences. In one case (B.2.1), the JHHS sub-lineage is captured by a non-major pangolin lineage designation.

Supplemental Figure 3. Illumina and Oxford Nanopore allele frequency comparison. (A) Variant frequencies from tiled amplicons sequenced on the Oxford Nanopore (ONT) and Illumina platforms. All variants at >0.02 allele frequency are shown. Uncalled variants are those not present in the consensus sequences from these samples. Grey shaded regions represent frequency threshold (25%) used to automatically reject candidate variants. Almost all discrepancies in frequency occur within homopolymer regions (red symbols). (B) Difference between allele frequencies across the two sequencing platforms. Position 3,037 (within a T-homopolymer) accounts for most large discrepancies in frequency.

Supplemental Figure 4. Common Oxford Nanopore sequencing issues. (A) Example of a T-homopolymer region in the SARS-CoV-2 genome (sample MDHP-00028). A large number of reads have deletions, resulting in a mixed alternate allele frequency. (B) Example of strand bias in Oxford Nanopore sequencing reads (sample MDHP-00028). A mutation only occurs in minus strand reads.

Supplemental Figure 5. Evolutionary divergence in geographic regions. Pairwise matrix containing average pairwise genetic distances within (bolded in the diagonal) and between sequences from various geographic regions including: the District of Columbia (JHHS-DC + DC other), Maryland (JHHS-MD + MD other), Virginia (VA), Louisiana (LA), Idaho (ID), New York (NY), California (CA), Washington (WA), and two representative global subsamples (Global 1K and 3K). Green-to-red color scale highlights the most (red) and least (green) divergent within or between average distances.

Pangolin key lineage

AA.1B

JHHS-DCJHHS-MD

B.1B.1.1B.1.2

2.0

USA/ID-UW-2255/2020

Malaysia/MKAK-CL-2020-5045/2020

USA/VA-DCLS-00011/2020

Russia/StPetersburg-3524/2020

Georgia/Tb-712/2020

Singapore/30/2020

Canada/ON_PHL2445/2020

Germany/BAV-MVP0060/2020

USA/ID-UW-4380/2020


USA/DC-CDC-9096/2020

Australia/VIC753/2020

Thailand/Bangkok-CONI-0115/2020

Switzerland/100116/2020

USA/NE-907/2020

Nigeria/OS016-CV3/2020

HongKong/HKPU89-2502/2020

USA/PA-MGSC17-04/2020

Poland/PL_P34/2020

USA/ID-UW-4448/2020

USA/MD-HP00044/2020

HongKong/HKPU2_1801/2020

Vietnam/CM295/2020

USA/NY-NYUMC564/2020

USA/PR-CDC-3578/2020

SARS-CoV-2/human/ZAF/R03006/2020

USA/WA-S243/2020

USA/MD-HP00154/2020

Canada/BC_13297/2020

England/20130034804/2020

USA/PA_2734/2020

USA/MD-HP00033/2020

USA/NJ-CDC-7300/2020

Portugal/CV62/2020

SouthKorea/KUMC02/2020

USA/NJ-NYUMC106/2020

SaudiArabia/KAUST-Madinah57/2020

USA/MA_0020/2020

USA/WA-S144/2020

USA/CA2/2020


USA/TX-HMH095/2020

USA/LA-SR0276/2020

Chile/Santiago_40/2020

Japan/SMU-0311S2/2020

USA/WA-S151/2020

USA/ID-UW-4427/2020

2019-nCoV/USA-CruiseA-15/2020

USA/NE-875/2020


USA/MD-HP00031/2020


USA/LA-SR0308/2020


Russia/Chelyabinsk-85311/2020

Spain/Valencia108/2020

Norway/1694/2020

Panama/328677/2020

USA/OR-UW-1937/2020

Israel/2023922/2020

USA/NH_0004/2020

Italy/AMC2-1245/2020

USA/WA-S97/2020

USA/WI-GMF-00018/2020

Philippines/PGC04/2020

USA/MD-HP00097/2020

Taiwan/CGMH-CGU-22/2020

USA/DC-HP00116/2020


Guam/GU_NHG_02/2020

USA/ID-UW-4486/2020


HongKong/VM20009579/2020

Hungary/MBL-002/2020

USA/WA-S81/2020

Sweden/20-04631/2020

Jordan/SR-042/2020

USA/NC_0025/2020


Timor-Leste/TL25/2020

USA/NC_6999/2020

USA/WA1-A12/2020

Luxembourg/LNS3089015/2020

USA/CT-Yale-010/2020

USA/WA-S290/2020

Portugal/PT0151/2020


Croatia/592_Osijek/2020

USA/WA-S213/2020

Jamaica/JM-CDC-0078/2020

Cambodia/0012/2020

USA/CA9/2020

Wuhan/HB-WH4-210/2020


USA/CA-SCCPHD-UC102/2020

Denmark/ALAB-SSI-1250/2020

Kuwait/KU09/2020


Thailand/Nonthaburi_2472/2020

USA/LA-SR0286/2020

Iceland/13/2020

Canada/BC_37_0-2/2020


Italy/TE6575/2020

Brazil/SP-10/2020


India/NIV-4369/2020

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USA/DC-HP00117/2020

USA/ID-UW-4424/2020

USA/LA-SR0164/2020

Vietnam/VNHN_0837/2020


USA/NE-886/2020

env/USA/MT-BWRF-0327/2020


Wuhan/IVDC-HB-05/2019


Italy/TE4953/2020

Colombia/INS-80123/2020

Ecuador/HEE-01/2020

USA/CA-CZB-1279/2020

USA/NC_0024/2020

Thailand/74/2020

USA/MD-HP00123/2020

Malaysia/188407/2020

USA/MD-HP00098/2020

Georgia/Tb-54/2020

USA/ID-UW-1925/2020

Brazil/SP-06/2020

Norway/1380/2020

HongKong/CUHK2/2020

USA/MD-HP00067/2020

USA/AK-PHL122/2020

USA/ID-UW-4357/2020

Switzerland/GR2988/2020

Kuwait/KU006/2020

France/IDF0571/2020

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USA/MD-HP00057/2020

Jordan/SR-039/2020

Gambia/GC19-026/2020

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France/GE1583/2020

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Finland/13M77/2020


USA/WA-S106/2020

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Brunei/5/2020

Indonesia/EJ-ITD853Sp/2020


USA/WY-WYPHL001/2020

Latvia/01/2020

Thailand/SI201712-NT/2020

USA/NC-CDC-0034/2020

USA/AZ1/2020

Austria/CeMM0002/2020


2019-nCoV/USA-CruiseA-18/2020

SouthAfrica/R05204/2020

Greece/140/2020

UnitedArabEmirates/L0184/2020

Uruguay/UY-3/2020

USA/CA-CZB011b/2020

Poland/PL_P27/2020

England/20138020704/2020

USA/ID-UW-3888/2020

Russia/Moscow-67609/2020

USA/DC-HP00007/2020

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Japan/OS-20-07-1/2020

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Netherlands/Tilburg_1363354/2020

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England/20134012504/2020

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Algeria/G0640_2265/2020

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USA/MN-MDH-313/2020

USA/MD-HP00127/2020

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Belgium/ULG-0189/2020

Japan/P5-3/2020


Israel/ISR_JP0320/2020

Brunei/4/2020

Kazakhstan/7263/2020

Oman/RESP-20-4736/2020

USA/SC_NHRC_01/2020

Iceland/46/2020



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NewZealand/20VR0993/2020

USA/LA-SR0275/2020

USA/IA_6394/2020

USA/CA-CDPH-UC3/2020


Qatar/QA19/2020


USA/CO-CDC-5610/2020

Slovenia/808/2020

Canada/ON_VIDO-01/2020

USA/MDH-5653/2020



Uganda/UG010/2020

Turkey/HSGM-1492/2020

USA/MD-HP00112/2020

USA/LA-CDC-1894/2020

Nigeria/OG007-CV22/2020


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Uganda/UG004/2020



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Iceland/32/2020

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Belgium/GHB-03021/2020


USA/MI-MDHHS-SC20133/2020

USA/DC-HP00139/2020


USA/MD-HP00038/2020

India/1-27/2020

USA/CA-CZB0100/2020

Poland/PL_P38/2020

Kazakhstan/NCB-3/2020

Portugal/IGC00009/2020

USA/WA-S95/2020

Chile/Punta_Arenas_16/2020

Sweden/20-05819/2020

USA/UT-021/2020

Iran/HGRC-01-IPI-8206/2020

USA/FL-CDC-2316/2020

USA/WI-GMF-00384/2020


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USA/IL-CDC-1732/2020

USA/NY-NYUMC75/2020

Kuwait/KU17/2020

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Uganda/UG003/2020


CostaRica/06/2020

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Ghana/2828_S6/2020

Wuhan/HB-WHCM-098/2020

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PuertoRico/CDC-S5/2020

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USA/CA-CZB-59X001/2020

Israel/701002666/2020

USA/NY-SURV0592/2020

DRC/KN-0060/2020

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Poland/PL_P24/2020

Finland/FIN-25/2020


USA/MD-HP00023/2020

France/HF1684/2020

Thailand/Bangkok_269/2020


USA/MD-HP00010/2020

Argentina/PAIS-A0003/2020


USA/MDH-5875/2020

USA/VA_6382/2020

Belgium/BA-02291/2020

USA/VI-CDC-3688/2020

Japan/DP0457/2020

Turkey/Istanbul-BezmCoV1/2020

USA/WA-UW-3932/2020

USA/WA-S107/2020

USA/MD-HP00024/2020

USA/MDH-9092/2020

Croatia/1146_Split/2020

Georgia/Tb-273/2020

USA/IL-NM098/2020

USA/IN_82003/2020

Netherlands/Utrecht_10036/2020

USA/NM-CDC-3589/2020

USA/IN_2001/2020

Sichuan/SC-MY-057/2020

USA/DC-HP00152/2020

USA/LA-SR0148/2020

USA/SC_NHRC_02/2020

USA/CA-CZB095/2020

USA/MD-HP00028/2020

Uruguay/UY-7/2020

USA/TX1/2020


Senegal/611/2020

Korea/KCDC2004/2020

USA/MD-HP00079/2020

Indonesia/JKT-EIJK03/2020

USA/MD-HP00149/2020


USA/WA-S113/2020


Korea/KCDC2002/2020

Ghana/3177_S12/2020

Israel/51137844/2020

USA/FL_9655/2020

HongKong/HKU-907b/2020

USA/LA-SR0210/2020

USA/IN_72003/2020

USA/MD-HP00141/2020

Croatia/8U-S17new/2020



Senegal/370/2020

USA/AZ-TG269848/2020

Israel/701002456/2020

USA/CruiseA-18/2020

Iceland/64/2020

USA/ID-UW-4418/2020

Denmark/ALAB-SSI254/2020

USA/NY-NYUMC41/2020

Italy/484/2020

USA/MD-HP00036/2020

Singapore/16/2020


Belgium/UGent-18/2020

USA/WA-S158/2020

USA/RI_0882/2020

France/ARA12371/2020

USA/WA-UW61/2020


USA/OH_0020/2020

nCoV-FIN-29-Jan-2020

USA/UT-090/2020

USA/WI-UW-08/2020

Pakistan/Manga-KPK/2020

Italy/PV-5314-B/2020

Italy/PV-5314-N/2020


Oman/RESP-20-2631/2020


Sweden/20-50312/2020

Luxembourg/Lux1/2020

Sichuan/SC-PHCC2-041/2020

Wuhan/WIV05/2019

USA/MD-CDC-0025/2020

USA/NY-Wadsworth-30164-01/2020

Jordan/SR-047/2020


England/20102088002/2020


CostaRica/03/2020


USA/UT-031/2020

USA/MD-HP00157/2020

Wuhan/IPBCAMS-WH-03/2019

Oman/RESP-20-3080/2020

Ireland/21145/2020

Malaysia/IMR_WC085/2020

env/USA/FL-UF11/2020

USA/VA_6389/2020

USA/SC_3569/2020

USA/LA-SR0149/2020

USA/MD-HP00118/2020

USA/KS-CDC-4589/2020


USA/OH-MDHHS-SC20370/2020


USA/LA-SR0271/2020

Spain/COV001084/2020

SouthAfrica/KRISP-06/2020

SARS-CoV-2/human/ITA/INMI1/2020


SouthKorea/KCDC07/2020

USA/NC-CDC-6999/2020

USA/MA_3653/2020




USA/ID-UW-4396/2020

USA/HI_7881/2020


USA/DC-HP00026/2020

USA/MDH-6612/2020


Brazil/SP-02/2020


USA/MD-HP00025/2020


Vietnam/19-02S/2020

USA/WA-UW-1731/2020

USA/CA-CZB072/2020

USA/WA-S43/2020

USA/WA-S47/2020

USA/CA-CZB0731/2020

England/200641094/2020

USA/AZ-TG268903/2020

Lebanon/S1_758/2020

Singapore/14/2020

England/20131103104/2020

USA/CA-SR0252/2020

Argentina/C121/2020

France/IDF0372/2020

USA/VA_6377/2020

Wuhan/Hu-1/2019

USA/CA-CZB0725/2020

Brunei/1/2020

France/IDF0386-islP1/2020



Thailand/NIH-15/2020

Singapore/13/2020

USA/HI_4970/2020

France/IDF0373/2020

Germany/NRW-06/2020

Finland/14M26/2020


USA/IL-NM065/2020

USA/WA-UW151/2020

Argentina/C3013/2020


USA/WA-S237/2020

USA/NY-NYUMC74/2020

USA/MA_3699/2020


Senegal/003/2020

France/ARA10910/2020


USA/MD-HP00156/2020


USA/MA_2652/2020

Nigeria/Lagos01/2020


USA/WA-UW75/2020

Mexico/CDMX-INCMNSZ_02/2020

France/IDF3081/2020

USA/CA6/2020

USA/WA-UW-4763/2020

USA/DC-HP00052/2020

USA/CA-CZB0110/2020

Guangdong/20SF118/2020


Japan/Hu_Kng_19-865/2020


Slovenia/12304/2020

USA/NJ_3592/2020

USA/WA-UW-4228/2020

USA/WI1/2020

USA/IN-CDC-2005/2020

USA/RI_0556/2020

France/IDF0626/2020

USA/ID-UW-2160/2020

Norway/2114/2020

Hungary/SRC-03670w/2020



USA/FL_5091/2020

Australia/QLD01/2020

Latvia/07/2020


USA/MD-HP00105/2020

USA/GA-EHC-083E/2020


Singapore/95/2020

Switzerland/BE6651/2020

India/NIV-5102/2020

Sweden/20-08151/2020

USA/WA-S194/2020

Japan/DP0058/2020

Ghana/1651_S3/2020

USA/ID-UW-4547/2020

USA/LA-SR0207/2020

SriLanka/COV38/2020

USA/LA-SR0289/2020

USA/ID-UW-4355/2020

CzechRepublic/IAB_10/2020

USA/LA-SR0162/2020


USA/MD-HP00101/2020

Japan/DP0464/2020


Malaysia/189332/2020

USA/NH_0008/2020

Vietnam/CM99/2020

USA/NY-Wadsworth-31302-01/2020


Italy/INMI2-N/2020


USA/GA_2741/2020

Greece/43_35679/2020


England/200690300/2020France/RA739/2020

USA/WI-GMF-00498/2020



India/1-31/2020

Mexico/CDMX-InDRE_01/2020

USA/MN-MDH-301/2020


USA/ID-UW-1938/2020



Denmark/ALAB-SSI410A/2020

USA/MN-CDC-0103/2020

USA/MN_0101/2020



USA/AR-CDC-2072/2020


Ghana/1659_S14/2020

Indonesia/EJ-ITD1238Sp/2020

Vietnam/VR03-38142/2020

USA/IA-CDC-8200/2020

USA/ID-UW-3892/2020

USA/CA-CZB077/2020

Norway/1495/2020

USA/LA-SR0145/2020

USA/DC-HP00138/2020

USA/WA-S5/2020

USA/ID-UW-4375/2020



Denmark/SSI-02/2020



Slovakia/SK-BMC1/2020


USA/WA3-UW1/2020


Brazil/DFBR-0001/2020

Greece/222_33921/2020


USA/CA1/2020

USA/CA_2602/2020

USA/MD-HP00055/2020


USA/CA-SR0256/2020

Singapore/12Clin/2020


Portugal/CV63/2020

USA/FL_9656/2020

USA/CA-CZB030/2020




USA/ID-UW-4400/2020

USA/ID-UW-2198/2020

Spain/Madrid-LP29/2020


Japan/SMU-0311S3/2020




SaudiArabia/KAUST-Makkah19/2020

Jordan/SR-056/2020

USA/MD-HP00140/2020

Australia/VPRL014/2020



USA/MD-HP00062/2020

CzechRepublic/ChVir1630/2020

Kuwait/KU12/2020




USA/WA-S8/2020



USA/AZ-TG270200/2020


USA/LA-SR0209/2020

India/NCDC-2514/2020

Singapore/1/2020

USA/MN-MDH-115/2020

USA/MD-HP00065/2020

England/20138024604/2020


USA/MD-HP00032/2020

SARS-CoV-2/human/TWN/CGMH-CGU-02/2020


Senegal/136/2020

USA/TX-HMH0196/2020

Japan/P4-7/2020


canine/HongKong/20-03695/2020




USA/NY-NYUMC54/2020

Lebanon/S9_764/2020


England/01/2020

Korea/KCDC2016/2020


USA/DC-HP00145/2020

USA/CA-CZB042/2020

USA/KS_4126/2020

France/PL1643/2020

USA/RI_0520/2020

USA/PA_2887/2020

USA/WA-UW-4329/2020

USA/MD-HP00148/2020

Sweden/20-08681/2020

Switzerland/AG0361/2020

DRC/82/2020

USA/WA-UW-2213/2020

Australia/QLDID922/2020

USA/WA-S408/2020

Canada/ON_SHSC-01/2020




env/USA/FL-UF3/2020

Kenya/NIC_569/2020

Israel/51141225/2020

Ecuador/HGSQ-USFQ-018/2020



USA/MD-HP00041/2020

England/201360049/2020

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Gambia/GC19-015/2020

Germany/NRW-09/2020

Singapore/19/2020



USA/ID-UW-4461/2020


USA/CruiseA-3/2020

USA/IN-Lilly-IPB0170-4bc20/2020

USA/WA-S99/2020

USA/FL_7169/2020

Germany/BavPat3-ChVir1020/2020

USA/WA-UW-1688/2020

USA/NY-WCMP11E04P/2020


USA/MD-HP00015/2020

USA/MD-HP00158/2020

Oman/RESP-20-837/2020

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USA/WA2/2020

Singapore/12/2020

Pakistan/KHI1/2020

USA/GA-EHC-115L/2020

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Singapore/18/2020

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USA/DC-HP00006/2020

Sichuan/SC-NJ-090/2020

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USA/MN-MDH-310/2020

USA/DC-HP00054/2020

Iran/HGRC-2-2162/2020


USA/WA-S119/2020

Italy/UniMI01/2020


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Norway/1811/2020

Switzerland/GE3895/2020

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Uruguay/Mdeo-1/2020

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Singapore/20/2020

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Chile/Rancagua_2/2020

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Iceland/99/2020

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Korea/KCDC2006/2020

Georgia/Tb-82/2020


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Egypt/NRC-01/2020

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Brazil/SP-03/2020

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Singapore/7/2020

USA/IL1/2020

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SriLanka/COV53/2020

Wuhan/WH01/2019

Senegal/016/2020

Germany/NRW-04/2020

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France/HF3598/2020

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USA/WA-UW145/2020


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Finland/FIN03032020B/2020

SARS-CoV-2/human/USA/CA-SCCPHD-UC14/2020

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Oman/RESP-20-1189/2020

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DRC/158/2020

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Brazil/ES-225/2020

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Supplemental Figure 6. Phylogenetic tree with all bootstrap values >65. Phylogenetic tree shown in Figures 3 and 4, but with bootstraps labeled on their corresponding nodes. Only bootstrap values greater than 65 are shown. Phylogenetic tree is colored as in Figure 4.

Supplemental Tables Supplemental Table 1. Aggregate JHHS diagnostic tests by date. Number of positive tests within the Johns Hopkins Health System on each day during March 2020. Supplemental Table 2. Aggregate sample metadata. Clinical metadata for all tested samples within the Johns Hopkins Health System, for all 143 samples sequenced in this study, and for the 114 patient samples that produced complete genomes. Results are grouped into appropriate bins to protect patient privacy. Supplemental Table 3. Sequencing metrics. Sample names and accession numbers (where relevant) for all 143 samples selected for sequencing alongside sequencing metrics. Clade assignments using the Pangolin and NextStrain nomenclature systems are also provided for each sample that resulted in a whole genome sequence. One sample (MDHP-00146) was submitted to public repositories prior to enforcing a strict threshold of at least 27,000 unambiguous nucleotides, and therefore has an accession number but was not included in this analysis. Supplemental Table 4. Single nucleotide polymorphisms present in JHHS sequences. Single nucleotide polymorphisms (with annotations) present in the 114 complete genomes generated in this study, alongside the number of samples containing each variant. Sites with IUPAC ambiguity codes due to mixed allele frequencies are also included. Supplemental Table 5. Accession numbers of samples used in phylogenetic analysis. Accession numbers and submitting lab information for all 1279 sequences included in our phylogenetic tree. Supplemental Table 6. Accession numbers of samples used in genetic distance analysis. Geographic group assignments for all sequences used in genetic distance analysis, listed by accession number. This table includes accession numbers for sequences included in the Global 3K dataset but were not included in the phylogenetic tree (which is based on the Global 1K dataset). Supplemental Table 7. Quartile values for pairwise genetic distances within each geographic region. Mean, median, min, max, Q1, and Q3 values for the pairwise genetic distance distributions of each geographic group used in our analysis.

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