Evidence map›Paper›PMID 36589229›Full record

ArticleFrontiers in molecular biosciences2022

Identification and mechanistic basis of non-ACE2 blocking neutralizing antibodies from COVID-19 patients with deep RNA sequencing and molecular dynamics simulations.

Alger M Fredericks, Kyle W East, Yuanjun Shi, Jinchan Liu, Federica Maschietto, Alfred Ayala, William G Cioffi, Maya Cohen, William G Fairbrother, Craig T Lefort and 6 more

Abstract read
In one paragraph

Article in Frontiers in molecular biosciences, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

4 citing papers in PubMed.

  1. Article
  2. Review
  3. Review
  4. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

16 authors.

Alger M FredericksDepartment of Surgery, Division of Surgical Research, The Miriam Hospital, Alpert Medical School of Brown University, Providence, RI, United States.
Kyle W EastDepartment of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, United States.
Yuanjun ShiDepartment of Chemistry, Yale University, New Haven, CT, United States.
Jinchan LiuDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States.
Federica MaschiettoDepartment of Chemistry, Yale University, New Haven, CT, United States.
Alfred AyalaDepartment of Surgery, Division of Surgical Research, Alpert Medical School of Brown University and Rhode Island Hospital, Providence, RI, United States.
William G CioffiDepartment of Surgery, Division of Surgical Research, Alpert Medical School of Brown University and Rhode Island Hospital, Providence, RI, United States.
Maya CohenDepartment of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, Alpert Medical School of Brown University and Rhode Island Hospital, Providence, RI, United States.
William G FairbrotherDepartment of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, United States.
Craig T LefortDepartment of Surgery, Division of Surgical Research, Alpert Medical School of Brown University and Rhode Island Hospital, Providence, RI, United States.
Gerard J NauDepartment of Medicine, Division of Infectious Disease, Alpert Medical School of Brown University and Rhode Island Hospital, Providence, RI, United States.
Mitchell M LevyDepartment of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, Alpert Medical School of Brown University and Rhode Island Hospital, Providence, RI, United States.
Jimin WangDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States.
Victor S BatistaDepartment of Chemistry, Yale University, New Haven, CT, United States.
George P LisiDepartment of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, United States.
Sean F MonaghanDepartment of Surgery, Division of Surgical Research, Alpert Medical School of Brown University and Rhode Island Hospital, Providence, RI, United States.

Funding

Using Genomic Epidemiology to Identify Transmission Patterns and Inform Intervention Strategies for Antibiotic-Resistant N. GonorrhoeaeP20GM121344 · NIGMS · MIRIAM HOSPITAL · PI FREDERICKS, ALGER M · 2018 to 2022
$9.4M
Mechanisms of Immune Dysfunction and Morbid Outcome in Response to Shock/SepsisR35GM118097 · NIGMS · RHODE ISLAND HOSPITAL · PI AYALA, ALFRED · 2016 to 2025
$6.3M
Selective Modulation of Neutrophils in Critical IllnessR35GM124911 · NIGMS · RHODE ISLAND HOSPITAL · PI CRAIG THOMAS LEFORT · 2017 to 2026
$3.8M
Improving Sepsis Care with Deep RNA Sequencing DataR35GM142638 · NIGMS · RHODE ISLAND HOSPITAL · PI Sean Farrell Monaghan · 2021 to 2026
$2.6M
Computational and Biochemical Studies of Temperature Effects on Allostery in the Imidazole Glycerol Phosphate Synthase (IGPS) from T. maritimaR01GM106121 · NIGMS · YALE UNIVERSITY · PI BATISTA, VICTOR S, LORIA, JOSEPH P · 2014 to 2021
$2.3M
Studies of Allostery between Multi-domain Proteins and Nucleic Acid ComplexesR01GM136815 · NIGMS · YALE UNIVERSITY · PI BATISTA, VICTOR S · 2021 to 2024
$1.4M
NIGMS NIH HHS P20 GM121344NIGMS NIH HHS R01 GM106121NIGMS NIH HHS R01 GM136815NIGMS NIH HHS R35 GM118097NIGMS NIH HHS R35 GM124911NIGMS NIH HHS R35 GM142638
6 · The paper itself

Abstract

Variants of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) continue to cause disease and impair the effectiveness of treatments. The therapeutic potential of convergent neutralizing antibodies (NAbs) from fully recovered patients has been explored in several early stages of novel drugs. Here, we identified initially elicited NAbs (Ig Heavy, Ig lambda, Ig kappa) in response to COVID-19 infection in patients admitted to the intensive care unit at a single center with deep RNA sequencing (>100 million reads) of peripheral blood as a diagnostic tool for predicting the severity of the disease and as a means to pinpoint specific compensatory NAb treatments. Clinical data were prospectively collected at multiple time points during ICU admission, and amino acid sequences for the NAb CDR3 segments were identified. Patients who survived severe COVID-19 had significantly more of a Class 3 antibody (C135) to SARS-CoV-2 compared to non-survivors (15059.4 vs. 1412.7,

Indexed as

antibodiesCOVID-19intensive careRNA sequencingsepsis

Identifiers

PMID36589229
PMCPMC9800910

What OpenQuestion holds

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LicenceCC BY
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.