Peer review of: Broadly neutralizing plasma antibodies effective against autologous circulating viruses in (2019)

Reviewers' Comments: 
 
Reviewer #1: 
Remarks to the Author: 
This is a paper describing a cohort of HIV-1-infected infants and young children who developed 
broadly neutralizing antibodies (bnAbs) and the characterization of their characteristics. This 
contributes to a growing body of literature that suggests infants may have different immunological 
tolerance thresholds and may be permissive for the development of bnAbs. However, I cannot support 
this paper in the present version as there is both overreach in the wording implying a strength of 
evidence that is not present and a lack of detail about many of the analyses that make interpretation 
of the data impossible for the reviewer. The data may be correct and the findings important, but as 
presented I cannot judge the strength of the case being made. 
 
1. Page 2 line 53: the statement that the data suggest that “similar bnAbs can be induced early with 
targeted vaccination” is not supported by the data shown. The data support that similar bnAbs *may* 
be elicited, but to say *can* would require a vaccination study. 
 
2. Figure 2C is overinterpreted. The text (p3 lines 59-60) states that “High viral load emerged as a 
negative driver of neutralization breadth”. High viral loads at the time of measurement were inversely 
correlated with breadth, but to say they were a driver would require more information than is 
presented, in particular, longitudinal data to show that viral loads were stable at the values shown. 
 
3. Figures 2DEF are confusing. First, cross-neutralizers is not defined in the text; cross-neutralization 
is described as correlating with GMT and other parameters, but I do not see where it is defined except 
in Fig S1 where it is shown as +/-. Second, a case is made for a difference between male and female 
cross-neutralizers, but Fig 2D and Fig 2E both show overlapping distributions, while Fig 2F makes no 
sense—how are the values calculated and why are the dots different size? Third, the results of a 
statistical test are given in the text, but it is not explained to which figure this refers or what test was 
applied. 
 
4. While I agree that the branching pattern shown in Fig S3 convincingly shows two circulating strains 
for Infant 709, the branching patterns for 704 and 706 are less convincing. With the absence of 
longitudinal data or deeper sampling, the patterns seen could easily be the result of undersampling. 
The data are suggestive, not definitive. This makes the claim of a strong association with multiple 
infection strains less convincing as well. This might be supported by a statistical analysis, but none is 
provided, and the interpretation of branching patterns appears to be visual inspection which could 
result in unintentional bias. Without all of the other data being presented in a manner similar to Fig 
S3, the reviewer is without data upon which to rest their judgement. On a side note, changing the 
colors of the branches between Figures 3 and S3 makes it hard to find the same infant in the two 
figures. In addition, in Fig 3, it is not clear where the data for CIN, 8BC, and 7BC come from as they 
do not appear in the tables or methods. 
 
 
M. Anthony Moody 
 
 
 
Reviewer #2: 
Remarks to the Author: 
 
 

The manuscript by Mishra, Sharma, Dobhal and colleagues builds on an emerging body of interesting 
data regarding the accelerated development of broadly neutralizing antibodies in pediatric HIV-
infected donors. Here the authors assess a pediatric cohort for broadly neutralizing antibodies, and 
perform some limited mapping of specificities and viral sequence analysis. 
 
Although there are some interesting observations in this paper, the analyses are generally fairly 
superficial and require additional work in order to substantially add to the HIV vaccine field. 
 
Line 27 - the authors have used to global panel (as many others do) but also supplemented this with 
seven local Indian viruses. This results in quite a considerable over-estimate of breadth in this cohort 
compared to similar studies, as these plasma appear to preferentially neutralize these Indian viruses 
(Fig 1). I do agree that the breadth in the four elite neutralizers is remarkable for that age and 
warrants a much more detailed investigation of these four donors. 
 
Line 28 – related to this, the authors claim that 19/47 (42% of donors) have cross-clade activity but 
this is often a consequence of neutralization of a single or two global viruses with low titer. This 
overstates the breadth of many of these donors. 
 
Line 40 – Fig 1E – it’s unclear how this analysis “confirms the validity of the panel and scoring system” 
 
Line 42 – the mapping of specificities is weak, and makes use of a single envelope backbone only. The 
high levels of V2 antibodies reported here may well be a viral attribute of this single env clone, HIV-
25710-2.43 (not well characterized in the literature). To be useful, the mapping needs to be 
significantly expanded. For example, as the authors mention, MPER antibodies are rare in children – is 
the breadth of donor AIIMS704 generally MPER-mediated or is that only true of HIV-25710-2.43 
neutralization? 
 
Line 59 – What do the authors mean by “antigenic saturation” in their cohort? 
Also - Muenchoff, STM, 2016 (a key description of pediatric broadly neutralizing antibodies not cited 
here) report a correlation between VL and broadly neutralizing antibodies – what could explain these 
discrepant results? Is this a consequence of donor age, with children <5 years old experiencing a 
decline in VL before this stabilizes? 
 
Line 70 – the authors state that they generated 30 SGA sequences per donor – why are only 4-10 
sequences per donor shown on the tree? Are other measures of viral diversity derived (Fig 3 B) from 
the full set or smaller datasets? 
 
Line 73 and title of paper - the authors argue that elite neutralizers are enriched for multivariant 
transmission. However, these sequences are not from the point of transmission and so multivariant 
transmission cannot be inferred. While AIIMS704 and 706 definitely show high levels of variability at 
this timepoint, this may well be a consequence of divergent escape pathways as has been shown for 
many donors with broadly neutralizing antibodies. Bootstraps should be added to the tree as a 
measure of statistical support. 
 
In addition, on lines 80-85 the authors (incorrectly in my view) define multivariant infection as 
infection by “two or more different strains”. With the exception of AIIMS709, this is not supported by 
Fig 3 where all other donors show phylogenetic linkage. 
 
Line 77 – “with long branch lengths suggestive of highly diverse infecting viruses”. This statement 
makes little sense. Please clarify. 
 

Line 89 – this is true for adults too. 
 
The section on phenotypic characterization of autologous clones is interesting, however no attempt is 
made to link the mapping with viral escape patterns. Furthermore, the description of autologous 
clones would benefit from a matched analysis of viral sequences. 
 
Line 100 and elsewhere – it is unclear to me why the authors focus on V2 germline targeting. The only 
mapping performed here is for one clone – whether V2 antibodies truly mediate breadth in this cohort 
has not been shown. Furthermore, as the authors themselves point out, this would require a detailed 
understanding of whether these envelopes have the capacity to trigger V2 precursors.