Table 3 Determining a single sensitivity threshold necessary and sufficient for predicting CXCR4-usage according to the combined 11/25 and net charge rule.

From: Position-specific automated processing of V3 env ultra-deep pyrosequencing data for predicting HIV-1 tropism

case

Criteria of the combined 11/25 and net charge rule for HIV-1 subtype B

retained threshold

  

25R and net charge* ≥ +5

net charge* ≥ +6

11R or 11K

25K

25R and net charge = +5

25R and net charge > +5†

net charge = +6

net charge > +6‡

1

x

     

position 11

2

 

x

    

position 25

3

  

x

   

maximum§

4

   

x

  

maximum†,§

5

    

x

 

maximum

6

     

x

maximum‡,

7

x

x

    

minimum#

8

x

 

x

   

minimum§,||

9

x

  

x

  

minimum†,§,||

10

x

   

x

 

minimum,**

11

x

    

x

minimum‡,,**

12

 

x

  

x

 

minimum,††

13

 

x

   

x

minimum‡,,††

14

x

x

  

x

 

minimum,‡‡

15

x

x

   

x

minimum‡,,‡‡

  1. *The V3 net charge was calculated by subtracting the number of negatively charged amino acids (D and E) from the number of positively charged ones (K and R).
  2. †The most pejorative positions harboring a positively charged residue were eliminated to reach the criterion << 25R and net charge = +5 >>. Alternatively, position 25 can be eliminated to arrive at the criterion << net charge = +6 >> if more favorable.
  3. ‡The most pejorative positions harboring a positively charged residue were eliminated to arrive at the criterion << net charge = +6 >>.
  4. §The most pejorative threshold between that of position 25 and those required for a net charge of +5 is used.
  5. The most pejorative threshold of the positions harboring a positively charged residue was used.
  6. #The least pejorative threshold between those of positions 11 and 25 is used.
  7. ||The least pejorative threshold between that of position 11 and those required for the << 25R and net charge = +5 >> criterion is used.
  8. **The least pejorative threshold between that of position 11 and those required for a net charge of +6 is used.
  9. ††The least pejorative threshold between that of position 25 and those required for a net charge of +6 is used.
  10. ‡‡The least pejorative threshold between those of positions 11, and 25, and those required for a net charge of +6 is used.
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