1. Epidemiology and Global Health
  2. Immunology and Inflammation
Download icon

A single, continuous metric to define tiered serum neutralization potency against HIV

  1. Peter Hraber  Is a corresponding author
  2. Bette Korber
  3. Kshitij Wagh
  4. David Montefiori
  5. Mario Roederer
  1. Los Alamos National Laboratory, United States
  2. New Mexico Consortium, United States
  3. Duke University Medical Center, United States
  4. National Institute of Allergy and Infectious Diseases, National Institutes of Health, United States
Research Article
Cite as: eLife 2018;7:e31805 doi: 10.7554/eLife.31805
6 figures, 2 tables and 1 additional file

Figures

Conceptual introduction to serum neutralization potency (NP).

(a) A hypothetical serum, which neutralizes tier 1A and some tier 1B viruses (red), but does not neutralize any tier 2 or 3 viruses (black), is assigned a neutralization potency (NP) of 1.1. (b) Another hypothetical serum may neutralize all tier 1A and B viruses and most tier 2 viruses, for NP of 2.8. In practice (c), the two outcomes do not segregate so clearly. Instead, positive and negative results among pseudoviruses are interspersed. Neutralization outcomes are scattered over the range of mean ID50s, and more sensitive viruses are enriched for positive neutralization. Logistic regression provides an objective way to distinguish neutralization outcomes. The neutralization outcome is treated as a probability (d). We use logistic regression to define the serum NP, which is the Env neutralization index (NI) value with 50% probability of neutralization that best separates neutralized and non-neutralized viruses.

https://doi.org/10.7554/eLife.31805.002
Figure 2 with 1 supplement
Neutralization potencies (NP) in the M-group panel of 225 Envs and 205 sera.

(a) Linear transformation of NSDP virus geometric mean ID50 neutralization titers provides a tiered scale, based on previous reports. Symbol colors indicate neutralization sensitivity, from ranked virus mean ID50s, and range from most (red) to least sensitive (grey). Envs identified for use in candidate subset panels that reproduce full virus panel NP values are labeled, with corresponding symbols colored black. We use the transformed values to compute serum NP. (b) Serum NPs are correlated with geometric mean ID50s per serum but, because of the transformation applied to viruses, range from about 1 to 4, consistent with the established Env tier classification scheme. Symbol colors show potency among ranked mean serum ID50s, and range from least (grey) to most potent (blue). Other colors indicate results from χ2 tests for non-zero slope, with Bonferroni corrections for 205 tests (red, experiment-wide p>0.1/205, that is per-comparison p>0.000488; magenta, experiment-wide p>0.05/205, per-comparison p>0.000244).

https://doi.org/10.7554/eLife.31805.003
Figure 2—figure supplement 1
Comparison of observed and bootstrap-resampled neutralization potency values.

(a) Serum NPs computed from the 225-Env panel (circles) and from 500 bootstrap-resampled replicate panels of 225 Envs, with replacement. The resampled distribution is summarized as the median and interquartile range (IQR) using a tick and bar, respectively. Symbol colors indicate results from χ2 tests for non-zero slope, using Bonferroni corrections for 205 tests (red, experiment-wide p>0.1/205, that is per comparison p>0.000488; magenta, experiment-wide p>0.05/205, per comparison p>0.000244). Results with adjusted p-values below 0.05 are colored by rank serum neutralization potency (grey to blue), as in Figure 2b. (b) Differences between resampled and observed NP values. Resampled NP median and IQR are shown, with the observed NP values subtracted.

https://doi.org/10.7554/eLife.31805.004
Neutralization outcomes and NP computation for a typical serum, SA.C37.

This serum was chosen for illustration because it represents the median serum potency. (a) Outcomes for each of 225 viruses are either neutralized (ID50 >50, red) or not (ID50 ≤50, black) and are scattered noisily over virus mean ID50s, as in the hypothetical example (Figure 1c). (b) Beeswarm plot of the same data summarizes the NI distribution (tier-scaled geometric mean ID50 per virus) by outcome. The χ2 p-value for significance of the slope is 4.79 × 10−12. A superimposed curve shows the inferred logistic function, and a vertical line indicates the NP at 2.5. Symbol color indicates virus neutralization sensitivity, as in Figure 2a.

https://doi.org/10.7554/eLife.31805.005
Figure 4 with 3 supplements
Panel-based NP estimates for a typical serum.

The serum SA.C37 (Figure 3) was chosen for illustration because it represents median serum potency. (a) Global virus panel of 11 Envs. Lasso-selected (b) 10- and (c) 20-Env panels. In each case, panel viruses are identified by name, and text annotations indicate the NP (top-right corner), and the p-value for the null hypothesis of no slope (center).

https://doi.org/10.7554/eLife.31805.006
Figure 4—figure supplement 1
Heatmap of NSDP ID50 values identifies panel Envs.

The Venn diagram summarizes set membership in global (11-Env) and lasso (10- and 20-Env) panels. Lasso identified 10 Envs that explained 47.2% of the deviance that would be explained by a fully saturated model (the maximum-likelihood solution, involving all Envs) and 20 Envs explained 80.8% of the deviance. The lasso set of 10 is fully contained within the larger set of 20 Envs. Adding more than 20 Envs gave ever smaller increases in the proportion of deviance explained (not shown). Text colors correspond to Env names in the heatmap. ID50 values in the heatmap are shaded according to the legend in the upper-right corner. Envs (rows) and sera (columns) in the heatmap were hierarchically clustered, with leaf order weighted to indicate geometric mean titers. Only the column dendrogram is shown. Serum and Env names are prefixed by clade.

https://doi.org/10.7554/eLife.31805.007
Figure 4—figure supplement 2
Concordance of neutralization index estimates.

NP values are highly correlated when comparing between holdout and panel Envs, and between each of the panels we evaluated. In each comparison, using Kendall’s τ, p<10−16. (a–c) Comparisons of neutralization indices from (a) 11-, (b) 10-, and (c) 20-Env panels with the much larger remaining holdout (non-panel) Envs. (d–f) Comparisons between NPs from the three panels described in the text. In each panel, points are colored to indicate p-values from panels depicted along the x-axis.

https://doi.org/10.7554/eLife.31805.008
Figure 4—figure supplement 3
Cumulative p-value distributions for three candidate panels.

Smaller p-values indicate lower chance of a false positive in inferring slope of the logistic regression is non-zero, that is the NP is well defined. Light- and dark-grey shaded regions identify p-values above 0.05 and 0.1, respectively. Results are from each of 205 sera in the NSDP panel, computed against 10-, 11-, and 20-Env panels.

https://doi.org/10.7554/eLife.31805.009
Neutralization potency analysis recapitulates mean titers and differences between progressors and long-term non-progressors (LTNP).

Scatter-plot compares geometric mean ID50 titers, computed from 20 Envs, with NP scores, computed using 10 Envs. Symbol color shows whether the serum was from LTNP or progressor. Open circles had p-values from χ2 testing of 0.1 or more, suggesting the NP scores were unreliably quantified. Separate beeswarm plots show results for mean ID50 and NP scores, stratified by group.

https://doi.org/10.7554/eLife.31805.010
Analysis of monoclonal bnAb combinations.

Increasing the number of bnAbs increases NP and slope. We used a cutoff IC50 of 0.1 µg/ml for 112 Envs and 27 bnAb combinations (Kong et al., 2015). (a) Neutralization potency (NP = –b0/b1, where b0 is intercept and b1 is slope of logistic function). (b) Slope (b1) of logistic function. Up to four bnAbs were combined per set. Set 1included PGT128, PG9, 10E8, and VRC07. Set 2 included 10.1074, PG9, 3BNC117, and 10E8. (PG9 and 10E8 were in both.) Letters A through F correspond to individual bnAbs and are used to label combinations, for example the four bnAbs combined in Set 1 are indicated as ACEF and in Set 2 as BCDE. p-Values indicate slope significance by χ2 test.

https://doi.org/10.7554/eLife.31805.013

Tables

Table 1
Fifteen Env-pseudotyped viruses in neutralization assays against sera from 50 vaccinated rabbits sampled 22 weeks after initial vaccination (boosted at week 4 and 20) with stabilized SOSIP trimers, (Torrents de la Peña et al., 2017) utilized in Table 2 to compare NP values using a cutoff ID50 of 50, breadth (% of Envs neutralized with an ID50 at least 50), and geometric mean titer (gmID50). 

These data appear in Table S4 of the original paper (Torrents de la Peña et al., 2017). A dash in Table 2 indicates ID50 below 20. Bold text in Table 2 indicates positive neutralization outcomes in NP calculations.

https://doi.org/10.7554/eLife.31805.011
Column in Table 2NameAccessionNISubtype
a25710–2.43EF1172712.04C
bZM197MDQ3885152.19C
cZM109FAY4241382.27C
dTV1.21HM2154372.32C
eREJOAY8354492.36B
fBJOX002000.03.2HM2153642.45CRF07
gTRO.11AY8354452.47B
hCE1176_A3FJ4444372.56C
i246-F3_C10_2HM2152792.56AC
jCH119.10EF1172612.61CRF07
kX1632_S2_B10FJ8173702.61B
lZM233M.PB6DQ3885172.63C
mWITOAY8354512.96B
nCE703010217_B6KC8941092.97A
oCNE55HM2154183.03CRF01
Table 2
Comparison of NP, breadth, and geometric mean ID50 for Envs (Torrents de la Peña et al., 2017) listed in Table 1.
https://doi.org/10.7554/eLife.31805.012
ImmunogenIDEnvNPPBreadthgmID50
Study C022-15abcdefghijklmno
BG505.6641569---2722----------1.050.00582011.3
BG505.6641570---28-----------1.050.00582010.7
BG505.6641571---71-----------1.730.0171711.4
BG505.6641572---30-----------1.050.00582010.8
BG505.6641573---75-----------1.730.0171711.4
BG505.v4.11574---12989----------1.930.02121313.7
BG505.v4.11575--21------------1.050.00582010.5
BG505.v4.11576---------------1.050.00582010.0
BG505.v4.11577--24------------1.050.00582010.6
BG505.v4.11578--264621-------43--1.050.00582013.7
BG505.v5.11584--2335--------44--1.050.00582012.7
BG505.v5.11585--21------------1.050.00582010.5
BG505.v5.11586--242720-------58--0.870.0831713.3
BG505.v5.11587----20----------1.050.00582010.5
BG505.v5.11588--285524----------1.730.0171712.7
BG505.v5.21589--2830-----------1.050.00582011.5
BG505.v5.21590--242227-------23--1.050.00582012.6
BG505.v5.21591--2231--------60--0.870.0831712.8
BG505.v5.21592--2328--------21--1.050.00582011.9
BG505.v5.21593--2424-----33-----1.050.00582012.2
Study C0119-15
BG505.v5.21819---------------1.050.00582010.0
BG505.v5.21820-----21-21-2623--25-1.050.00582013.2
BG505.v5.21821---30-----------1.050.00582010.8
BG505.v5.21822-------25-------1.050.00582010.6
BG505.v5.21823---35-26--283625--30241.050.00582016.4
v5.2+211 C-433C1824---72-----------1.730.0171711.4
v5.2+211 C-433C1825--7630-----------1.880.0131712.3
v5.2+211 C-433C1826--4630-----22-----1.050.00582012.6
v5.2+211 C-433C1827--755066----27--40--2.000.01672016.9
v5.2+211 C-433C1828--37------------1.050.00582010.9
BG505.v6182929-3642-25-24302725--26-1.050.00582018.9
BG505.v6183031-80974229-26322931--29212.040.01341325.6
BG505.v61831--16016222----------2.040.01341315.3
BG505.v6183229-6546847----------2.040.01341317.4
BG505.v61833--472333----------1.050.00582012.7
Study C0045-15
ZM197M.6641649261622335---323737----222.010.00765720.0
ZM197M.6641650---20-----------1.050.00582010.5
ZM197M.6641651---35---21-------1.050.00582011.4
ZM197M.664165223365-35---452427-----2.010.00765718.3
ZM197M.6641653-213138-----------1.050.00582012.4
ZM197M.v4.21654-------21-------1.050.00582010.5
ZM197M.v4.21655-4860-21-----------2.010.00765715.9
ZM197M.v4.2165625282069-----------1.730.0171713.6
ZM197M.v4.21657---------------1.050.00582010.0
ZM197M.v4.21658---32-----------1.050.00582010.8
Study C0120-15
ZM197M.v5.21874-10104953-21--27------2.110.008281319.0
ZM197M.v5.21875-15387604523--24------2.230.003892019.3
ZM197M.v5.21876246435696820--33------2.190.00792019.1
ZM197M.v5.21877-452037-25--382225--27251.050.00582018.7
ZM197M.v5.21878-1142168-31--522925--27252.070.02192021.9

Additional files

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Download citations (links to download the citations from this article in formats compatible with various reference manager tools)

Open citations (links to open the citations from this article in various online reference manager services)