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. 2014 Nov;88(21):12623–12643. doi: 10.1128/JVI.01705-14

TABLE 3.

Correlation of plasma Env hypervariable loop properties (length, net charge, and number of potential N-linked glycosylation sites) with geometric mean ID50 per plasma sample

Property All dataa
 Positive valuesb
 No-low-titer plasma samplesc
 Positive and no-low-titer plasma samplesd
τe pf qg τ p q τ p q τ p q
V1 lengthh 0.08 0.144 0.273 0.06 0.258 0.394 0.15 0.017 0.062* 0.13 0.027 0.088*
V1 netchgi −0.02 0.696 0.696 0.01 0.804 0.739 0.00 0.961 0.770 0.01 0.827 0.742
V1 glycosj 0.09 0.118 0.240 0.11 0.064 0.155 0.18 0.006 0.034** 0.18 0.005 0.031**
V2 length 0.10 0.068 0.163 0.10 0.068 0.163 0.04 0.561 0.623 0.03 0.609 0.646
V2 netchg 0.15 0.011 0.048** 0.12 0.038 0.111 0.16 0.012 0.051* 0.13 0.053 0.136
V2 glycos 0.01 0.931 0.763 −0.01 0.898 0.763 −0.03 0.691 0.694 −0.04 0.569 0.627
V1V2 length 0.13 0.016 0.061* 0.13 0.017 0.062* 0.17 0.004 0.031** 0.17 0.005 0.031**
V1V2 netchg 0.06 0.259 0.394 0.07 0.180 0.310 0.10 0.107 0.223 0.10 0.135 0.261
V1V2 glycos 0.09 0.110 0.225 0.09 0.108 0.223 0.16 0.016 0.061* 0.14 0.030 0.093*
V4 length −0.03 0.591 0.633 −0.07 0.205 0.336 −0.04 0.486 0.568 −0.07 0.228 0.363
V4 netchg −0.01 0.835 0.742 0.02 0.747 0.729 0.00 0.987 0.775 0.03 0.658 0.682
V4 glycos −0.07 0.265 0.395 −0.08 0.165 0.294 −0.01 0.925 0.763 −0.01 0.852 0.746
V5 length 0.01 0.876 0.758 −0.01 0.906 0.763 0.08 0.227 0.363 0.05 0.475 0.566
V5 netchg −0.01 0.814 0.739 −0.01 0.927 0.763 0.03 0.650 0.679 0.01 0.920 0.763
a

Censored values taken as given, i.e., placeholder constants of 10 for ID50s below 20 (n = 170).

b

Censored values treated as missing, i.e., only positive assay results were used (n = 170).

c

Plasma samples with geometric mean ID50 below 20 were excluded from these comparisons (n = 129).

d

Both plasma samples with low geometric mean ID50s and censored values were excluded (n = 129).

e

Kendall's τ as computed by the eponymous R package.

f

Two-sided P value for the null hypothesis of no correlation.

g

False-discovery rates computed from 360 P values by the q-value package. Significance levels: *, q < 0.10; **, q < 0.05.

h

Hypervariable loop boundaries are defined in Text S2 in the supplemental material and are not simply cysteine-cysteine.

i

Net charge, i.e., number of K, H, and R sites minus the number of D and E sites.

j

Number of potential N-linked glycosylation sites following the Nx[ST] motif, with x not P.