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Table 3 At most sites of selection identified using ExpCM, mutations affect drug resistance or immune escape

From: Identification of positive selection in genes is greatly improved by using experimentally informed site-specific models

Gene

Site

Affects biologically relevant phenotype?

β-lactamase

35

No evidence implicating this site in resistance [15]

 

48

No evidence implicating this site in resistance [15]

 

104

E104K involved in β-lactam resistance [15]

 

112

No evidence implicating this site in resistance [15]

 

164

R164C, R164H, and R164S involved in β-lactam resistance [15]

 

182

M182T potentiates resistance [15]

 

238

G238S involved in β-lactam resistance [15]

 

240

E240K involved in β-lactam resistance [15]

 

244

R244C, R244H, and R244S involved in inhibitor resistance [15]

NP

20

In a T-cell epitope [94]

 

101

In an antibody epitope [95]

 

105

In a T-cell epitope [96]

 

131

Not part of known immune epitope

 

290

In an antibody epitope [97]

 

319

Not part of known immune epitope

 

371

In an antibody epitope [98, 99]

 

375

E375G interacts with T-cell escape mutation at 384 [58, 100]

 

384

R384G and R384K are T-cell escape mutations [38, 100]

 

422

K422R is a T-cell escape mutation [101]

HA

138

Contacts antigenic-site residues defined by the experiments of [40]

 

189

Contacts antigenic-site residues defined by the experiments of [40]

 

225

An antigenic site residue defined by the experiments of [40]; also affects receptor-binding specificity and so known to undergo substitutions both during host adaptation and viral passaging in the lab [8487]