Longitudinal Evolution of the HIV Env Glycoprotein
Longitudinal Env evolution analyses were performed as described (12 (link)). Briefly, LASSIE (https://github.com/phraber/lassie) was used to identify amino acid/glycan mutations under selection, using 80% or higher loss of the transmitted virus sequence as the cutoff. The webtool AnalyzeAlign was used to calculate sequence logos (https://www.hiv.lanl.gov/content/sequence/ANALYZEALIGN/analyze_align.html) that show evolution at such sites. Glycan shield mapping was performed using the Glycan Shield Mapping tool (https://www.hiv.lanl.gov/content/sequence/GLYSHIELDMAP/glyshieldmap.html) (56 (link)). Hypervariable loops from longitudinal Envs were characterized using alignment-free characteristics (https://www.hiv.lanl.gov/content/sequence/VAR_REG_CHAR/index.html), such as length, number of glycans, and net charge. Hypervariable loop positions were identified based on HXB2 numbering:132 to 152 for hypervariable V1,185 to 190 for hypervariable V2, 396 to 410 for hypervariable V4, and 460 to 465 for hypervariable V5.
Bibollet-Ruche F., Russell R.M., Ding W., Liu W., Li Y., Wagh K., Wrapp D., Habib R., Skelly A.N., Roark R.S., Sherrill-Mix S., Wang S., Rando J., Lindemuth E., Cruickshank K., Park Y., Baum R., Carey J.W., Connell A.J., Li H., Giorgi E.E., Song G.S., Ding S., Finzi A., Newman A., Hernandez G.E., Machiele E., Cain D.W., Mansouri K., Lewis M.G., Montefiori D.C., Wiehe K.J., Alam S.M., Teng I.T., Kwong P.D., Andrabi R., Verkoczy L., Burton D.R., Korber B.T., Saunders K.O., Haynes B.F., Edwards R.J., Shaw G.M, & Hahn B.H. (2023). A Germline-Targeting Chimpanzee SIV Envelope Glycoprotein Elicits a New Class of V2-Apex Directed Cross-Neutralizing Antibodies. mBio, 14(1), e03370-22.
Corresponding Organization : University of Pennsylvania
Other organizations :
Los Alamos National Laboratory, Duke University, The Wistar Institute, Scripps Research Institute, Centre Hospitalier de l’Université de Montréal, Université de Montréal, Bioqual, National Institute of Allergy and Infectious Diseases, National Institutes of Health, San Diego Biomedical Research Institute, Ragon Institute of MGH, MIT and Harvard
LASSIE (https://github.com/phraber/lassie) to identify amino acid/glycan mutations under selection, using 80% or higher loss of the transmitted virus sequence as the cutoff
AnalyzeAlign webtool (https://www.hiv.lanl.gov/content/sequence/ANALYZEALIGN/analyze_align.html) to calculate sequence logos that show evolution at identified sites
Glycan Shield Mapping tool (https://www.hiv.lanl.gov/content/sequence/GLYSHIELDMAP/glyshieldmap.html) to perform glycan shield mapping
Alignment-free characteristics (https://www.hiv.lanl.gov/content/sequence/VAR_REG_CHAR/index.html) to characterize hypervariable loops from longitudinal Envs
dependent variables
Amino acid/glycan mutations under selection
Sequence evolution at identified sites
Glycan shield mapping
Characteristics of hypervariable loops (length, number of glycans, net charge)
control variables
Longitudinal Env evolution analyses were performed as described (12 (link))
controls
No explicit mention of positive or negative controls
Annotations
Based on most similar protocols
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