Table 2 Lineage defining mutations and their frequency in the index case (NYCPHL-002130) and named contact partner (NYCPHL-002461).

From: Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City

Lineage

Defining mutations

Frequency

NYCPHL-002130

NYCPHL-002461

B.1

C241T

0.940

0.916

 

C3037T

0.939

0.934

 

C14408T

0.966

0.931

 

A23403G

0.949

0.945

Alpha

C913T

0.946

0.736

 

C3267T

0.973

0.755

 

A5388C

0.949

0.761

 

C5986T

0.983

0.771

 

T6954C

0.977

0.787

 

ORF1a: Δ3675-3677

0.983

0.806

 

C14676T

0.945

0.625

 

C15279T

1.000

0.772

 

T16176C

0.985

0.785

 

S: Δ69-70

1.000

0.983

 

S: Δ144

0.990

0.978

 

A23063T

0.944

0.776

 

C23271A

0.968

0.737

 

C23604A

0.902

0.711

 

C23709T

0.939

0.780

 

T24506G

0.971

0.766

 

G24914C

0.947

0.751

 

C27972T

0.978

0.706

 

G28048T

0.982

0.723

 

A28111G

0.978

0.718

 

G28280C

0.945

0.726

 

A28281T

0.963

0.727

 

T28282A

0.963

0.736

 

C28977T

0.962

0.704

Epsilon

C1059T

0.000

0.214

 

A12878G

0.000

0.172

 

G17014T

0.000

0.169

 

G21600T

0.000

0.170

 

G22018T

0.000

0.124

 

T22917G

0.000

0.181

 

T24349C

0.000

0.164

 

G25563T

0.000

0.178

 

C26681T

0.000

0.182

 

G27890T

0.000

0.235

 

A28272T

0.000

0.000

 

C28887T

0.000

0.227

  1. Δ in-frame codon deletion.
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