SARS-CoV-2 Cryptic Lineage Visualizations

CA-1

California

Samples detected: 3
Genome coverage: 47.56%
Total mutations: 123
Population: 4,000,000
Last detected: September 30, 2023

Predicted Parent lineage: AY.103

Timeline (2020-2025)

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CA-2

California

Samples detected: 3
Genome coverage: RBD-only
Total mutations: 15 (RBD only)
Population: Unknown
Last detected: December 31, 2021

Predicted Parent lineage: B.1

Timeline (2020-2025)

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CA-3

California

Samples detected: 1
Genome coverage: 65%
Total mutations: 45
Population: 13,754
Last detected: July 22, 2025

Predicted Parent lineage: B.1.617.2

Timeline (2020-2025)

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CH-1

Switzerland

Samples detected: 6
Genome coverage: 44.41%
Total mutations: 59
Population: unknown
Last detected: July 01, 2021

Predicted Parent lineage: B.1.416.1

Timeline (2020-2025)

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CO-1

Colorado

Samples detected: 5
Genome coverage: 11.43%
Total mutations: 49
Population: 53,356, 268,004
Last detected: March 01, 2022

Predicted Parent lineage: AY.4

Timeline (2020-2025)

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CO-2

Colorado

Samples detected: 2
Genome coverage: 41%
Total mutations: 190
Population: 15,000
Last detected: July 31, 2024

Predicted Parent lineage: BA.1

Timeline (2020-2025)

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FL-1

Florida

Samples detected: 2
Genome coverage: 20.13%
Total mutations: 8
Population: 776,150
Last detected: July 31, 2022

Predicted Parent lineage: B.1.533

Timeline (2020-2025)

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FL-2

Florida

Samples detected: 2
Genome coverage: 25.44%
Total mutations: 69
Population: 85,700
Last detected: January 01, 2023

Predicted Parent lineage: AY.35

Timeline (2020-2025)

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FL-3

Florida

Samples detected: 3
Genome coverage: 70%
Total mutations: 366
Population: 776,150
Last detected: June 15, 2024

Predicted Parent lineage: B.1.1.7

Timeline (2020-2025)

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FL-4

Florida

Samples detected: N/A
Genome coverage: 47%
Total mutations: 473
Population: 212,065
Last detected: May 06, 2025

Predicted Parent lineage: B.1

Timeline (2020-2025)

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GA-1

Georgia

Samples detected: 14
Genome coverage: 52%
Total mutations: 404
Population: 190,000
Last detected: July 01, 2025

Predicted Parent lineage: B.1.1.28

Timeline (2020-2025)

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ID-1

Idaho

Samples detected: 1
Genome coverage: RBD-only
Total mutations: 21 (RBD only)
Population: 50, 0
Last detected: August 05, 2025

Predicted Parent lineage: BQ.1.1

Timeline (2020-2025)

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IL-1

Illinois

Samples detected: 38
Genome coverage: 60%
Total mutations: 58
Population: 164,781
Last detected: June 13, 2022

Predicted Parent lineage: P.1

Timeline (2020-2025)

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IL-2

Illinois

Samples detected: 3
Genome coverage: 60%
Total mutations: 155
Population: 4,480
Last detected: March 01, 2022

Predicted Parent lineage: B.1

Timeline (2020-2025)

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IL-3

Illinois

Samples detected: 6
Genome coverage: 40%
Total mutations: 70
Population: 1,134,897
Last detected: June 30, 2024

Predicted Parent lineage: XBB.1

Timeline (2020-2025)

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KY-1

Kentucky

Samples detected: 8
Genome coverage: 38.75%
Total mutations: 59
Population: 55,928
Last detected: June 01, 2022

Predicted Parent lineage: AY.3

Timeline (2020-2025)

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MD-1

Maryland

Samples detected: 33
Genome coverage: 71%
Total mutations: 193
Population: 78,365
Last detected: January 09, 2025

Predicted Parent lineage: AY.103

Timeline (2020-2025)

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MI-1

Michigan

Samples detected: 5
Genome coverage: 73.97%
Total mutations: 200
Population: unknown
Last detected: May 01, 2023

Predicted Parent lineage: B.1.1.7

Timeline (2020-2025)

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MO-1

Missouri

Samples detected: 8
Genome coverage: RBD-only
Total mutations: 5 (RBD only)
Population: unknown
Last detected: April 30, 2021

Predicted Parent lineage: B.1

Timeline (2020-2025)

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MO-2

Missouri

Samples detected: 11
Genome coverage: RBD-only
Total mutations: 15 (RBD only)
Population: unknown
Last detected: October 04, 2022

Predicted Parent lineage: B.1

Timeline (2020-2025)

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MT-1

Montana

Samples detected: 1
Genome coverage: 29%
Total mutations: 91
Population: 8,000
Last detected: April 06, 2022

Predicted Parent lineage: B.1.617.2

Timeline (2020-2025)

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NC-1

North Carolina

Samples detected: 3
Genome coverage: N/A
Total mutations: 160
Population: 182,501
Last detected: December 29, 2023

Predicted Parent lineage: B.1

Timeline (2020-2025)

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NE-1

Nebraska

Samples detected: 61
Genome coverage: 13%
Total mutations: 116
Population: 100,000
Last detected: July 30, 2025

Predicted Parent lineage: B.1.160

Timeline (2020-2025)

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NH-1

New Hampshire

Samples detected: 4
Genome coverage: 50%
Total mutations: 206
Population: 40,000
Last detected: May 05, 2025

Predicted Parent lineage: BA.1.9

Timeline (2020-2025)

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NJ-1

New Jersey

Samples detected: 4
Genome coverage: 69%
Total mutations: 225
Population: 1,500,000
Last detected: April 01, 2024

Predicted Parent lineage: Unknown

Timeline (2020-2025)

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NL-1

Netherlands

Samples detected: 20
Genome coverage: 59.33%
Total mutations: 96
Population: 67,890
Last detected: September 01, 2022

Predicted Parent lineage: AY.43

Timeline (2020-2025)

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NY-1

New York

Samples detected: 15
Genome coverage: 63.47%
Total mutations: 91
Population: 70,470
Last detected: February 01, 2022

Predicted Parent lineage: B.1.2

Timeline (2020-2025)

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NY-10

New York

Samples detected: 10
Genome coverage: RBD-only
Total mutations: 18 (RBD only)
Population: Unknown
Last detected: February 28, 2022

Predicted Parent lineage: B.1

Timeline (2020-2025)

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NY-11

New York

Samples detected: 5
Genome coverage: RBD-only
Total mutations: 17 (RBD only)
Population: Unknown
Last detected: February 14, 2022

Predicted Parent lineage: B.1.1.7

Timeline (2020-2025)

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NY-12

New York

Samples detected: 1
Genome coverage: 53%
Total mutations: 208
Population: 649,549
Last detected: September 24, 2024

Predicted Parent lineage: BA.2?

Timeline (2020-2025)

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NY-13

New York

Samples detected: 1
Genome coverage: 48%
Total mutations: 191
Population: 649,549
Last detected: September 22, 2024

Predicted Parent lineage: B.1.1?

Timeline (2020-2025)

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NY-2

New York

Samples detected: 2
Genome coverage: 37.39%
Total mutations: 67
Population: Unknown
Last detected: July 31, 2021

Predicted Parent lineage: B.1.336

Timeline (2020-2025)

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NY-3

New York

Samples detected: 4
Genome coverage: 35.96%
Total mutations: 92
Population: Unknown
Last detected: August 01, 2021

Predicted Parent lineage: B.1.503

Timeline (2020-2025)

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NY-4

New York

Samples detected: 3
Genome coverage: 22.83%
Total mutations: 26
Population: 848,328
Last detected: August 01, 2023

Predicted Parent lineage: D.2

Timeline (2020-2025)

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NY-5

New York

Samples detected: 6
Genome coverage: 35.58%
Total mutations: 151
Population: 684,569
Last detected: July 01, 2023

Predicted Parent lineage: B.1.623

Timeline (2020-2025)

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NY-6

New York

Samples detected: 4
Genome coverage: 24.17%
Total mutations: 58
Population: 728,123
Last detected: June 01, 2023

Predicted Parent lineage: B.1.1.7

Timeline (2020-2025)

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NY-7

New York

Samples detected: 4
Genome coverage: 21.46%
Total mutations: 26
Population: 588,772
Last detected: September 01, 2023

Predicted Parent lineage: R.1

Timeline (2020-2025)

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NY-8

New York

Samples detected: 7
Genome coverage: RBD-only
Total mutations: 22 (RBD only)
Population: Unknown
Last detected: February 28, 2022

Predicted Parent lineage: B.1

Timeline (2020-2025)

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NY-9

New York

Samples detected: 9
Genome coverage: RBD-only
Total mutations: 20 (RBD only)
Population: Unknown
Last detected: October 18, 2021

Predicted Parent lineage: B.1

Timeline (2020-2025)

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OH-1

Ohio

Samples detected: 38
Genome coverage: 44.38%
Total mutations: 193
Population: 654,817, 14,000
Last detected: June 01, 2023

Predicted Parent lineage: B

Timeline (2020-2025)

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OH-2

Ohio

Samples detected: 30
Genome coverage: 50%
Total mutations: 256
Population: 313,158
Last detected: April 13, 2025

Predicted Parent lineage: BA.1.1

Timeline (2020-2025)

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SC-1

South Carolina

Samples detected: 1
Genome coverage: 76%
Total mutations: 172
Population: 12,000
Last detected: July 22, 2024

Predicted Parent lineage: B.1.617.2

Timeline (2020-2025)

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TX-1

Texas

Samples detected: 1
Genome coverage: 68%
Total mutations: 242
Population: 15,000
Last detected: June 02, 2025

Predicted Parent lineage: BA.1

Timeline (2020-2025)

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TX-2

Texas

Samples detected: 1
Genome coverage: 24%
Total mutations: 86
Population: 1,000,000
Last detected: July 01, 2025

Predicted Parent lineage: BA.1

Timeline (2020-2025)

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UK-1

United Kingdom

Samples detected: 48
Genome coverage: 50.28%
Total mutations: 142
Population: unknown
Last detected: February 01, 2022

Predicted Parent lineage: B.1.566

Timeline (2020-2025)

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WI-1

Wisconsin

Samples detected: 81
Genome coverage: 31.72%
Total mutations: 133
Population: unknown
Last detected: August 01, 2023

Predicted Parent lineage: B.1.234

Timeline (2020-2025)

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SARS-CoV-2 Cryptic Lineage Visualizations

Summary Statistics

Frequent Mutations Across All Lineages